I did my masters research project with Prof X. While doing this I joined his lab, where he used to ask me to do random tasks i.e. taking part in different projects, conducting lectures to undergrad students, help him preparing presentations, doing literature reviews not related to my project. I did all those things because of my curiosity and passion for learning as many things as I could. Unfortunately, this delayed my progress in my masters research project.

The Prof. X seemed not at all concerned not only about me but also his other students, except when he wanted us to publish. Although the research field was new to me and I had to do everything on my own and I learned a lot. In the end, he was quite happy and satisfied with my work. He offered me PhD position at his lab but having bad experience with him, I politely refused that right now I don't have any plan to pursue my PhD.

After that, I could notice he is very cold towards me. During my writing stage, he continuously burdened me more with different tasks related to lab. Moreover, after submission he totally ignored to pass the examiner's names to faculty and it delayed my masters results further two months, even though I requested him multiple times. Once I came to know about this delay through faculty, I told him very politely that how can he do that? He just said (laughingly): sorry I forgot about it.

This is not the first time I found him selfish and not consistent while having no concern about any of his student.


Now, I am applying for PhD position and I need references. I have other other faculty members with whom I have worked with or taken courses and they are willing to witness my motivation and good performance. The problem is that they require one of the referee must be the main research supervisor, in my case Prof X. I don't trust Prof. X in this matter. What should I do now?

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    You say that "they require one of the referee must be the main research supervisor". Let's suppose that you have two friends (A and B) who are also willing to join this PhD. A's master supervisor passed away a few months ago. B's master supervisor joined an expedition in Antarctica and won't return in the next months. What will the PhD evaluation committee (or whoever is there to receive the references) do in these cases? My intention with this question is to find out what happens when the master supervisor simply won't and can't provide a reference. Commented Nov 22, 2015 at 12:49
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    @VictorStafusa The analogy with the death of a supervisor is a special case and rather obsolete in this context. The selection committee should be informed and obviously they will assess the student based on his work and other recommendation letters.
    – Sathyam
    Commented Nov 22, 2015 at 12:57
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    The problem is that they require one of the referee must be the main research supervisor — Have you considered applying to a department that does not have this requirement?
    – JeffE
    Commented Dec 17, 2015 at 18:41
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    Just ask for two different reference letters and read one of them to make sure if he has written something to lower your reputation.
    – padawan
    Commented Jan 5, 2016 at 2:01
  • 1
    See What should I do if someone answers my question. Please follow those suggestions, and don't edit "thanks" into the body of your question; we are trying to build a library of focused, useful questions and answers here, with as little "chat" as possible.
    – ff524
    Commented Aug 10, 2016 at 6:14

9 Answers 9


If you submit an application with a bad reference, it will quite probably sink your application. On the other hand, simply ignoring the requirement in the application may lead to a desk reject.

However, if obtaining a good reference from your advisor is not going to happen, you should probably address that up front in your statement of purpose and include the reference anyway. Disclose, in a neutral fashion, that you had difficulties with your previous supervisor, and focus on what you learned from that. If you can show in your SoP that you can endure challenging situations, and even grow from them, while also showing you are able to conduct high quality research, this may outweigh not having the critical reference.


  • It meets the requirements of the application (if, indeed, you have verified that this is a hard requirement)
  • It demonstrates that you can endure challenges in research, as you will inevitably face more during your PhD (just hopefully of a different nature)
  • It shows maturity in your application (by favouring openness and transparency)


  • It includes a weak reference letter in your application, if you can even persuade your advisor to write it
  • It risks presenting (rather than concealing) less savoury characteristics of your past research profile, which shows that you're not a "golden," flawless candidate.
  • The impression here and in other answers is that a bad reference is fatal to an application. Is this really true? My gut feeling is that selection committees are pretty shrewd, and they will be able to spot if a reference is unfairly negative. However, I've not been on a selection committee myself so perhaps that is naive... Commented Dec 18, 2015 at 12:00

I assume that Prof. X would be known in the field that you work in. In that case, their behaviour will probably also be known to their colleagues. For the list of references I would give people I expected good references from. In the cover letter, I would mention that Prof. X was my academic supervisor and could be contacted, but that the references listed were my preferred references.

Be careful not to say anything rude about Prof. X. And don't complain too much about your experiences, or you would sound like someone who might be trouble. Just say who are your preferred references, and let the committee decide for themselves whether to go with your preferences or follow their own guidelines. If they go against your wishes and get a bad reference (or no reference), they won't be surprised, and hopefully they will also have gotten all the references you really recommended as well. But the committee might also respect your wishes.

I agree that this sounds like a bad situation, and you might want to warn juniors in the lab about your experience so they can transfer if they agree with you. Have you spoken to people who were senior PhD students when you came in, and ask how their experience went? It may be that you are overly worried now, and that in fact your supervisor writes excellent letters. You should probably do this before any of the other steps suggested above.

  • Have you spoken to people who were senior PhD students when you came in, and ask how their experience went? It may be that you are overly worried now, and that in fact your supervisor writes excellent letters. You should probably do this before any of the other steps suggested above. This is a great idea because OP is having trouble anticipating the main research advisor's behavior, and the letter is closed to the OP. The standard code language ("Would you be comfortable writing me a letter of recommendation") can't be counted on to give reliable results in the case of an advisor who... Commented Dec 20, 2015 at 13:53
  • behaves erratically. I would add to Joanna's answer: OP stated, "The Prof. X seemed not at all concerned not only about me but also his other students, except when he wanted us to publish," and said that Prof. X delayed the masters by two months by not carrying out a simple required communication step -- and then laughed about it. If Prof. X cannot carry out his advisorly duties reliably, then OP should put the problem squarely in the department's lap. A department administrator can sound out Prof. X, and send a departmental clarification letter if need be. Commented Dec 20, 2015 at 13:54

I'm sad to say but you are in very bad spot right now. From your description,it looks like that professor suffers from bad case of inflated ego combined with very petty and vengeful personality. To hold back someone out of pure spite is quite bad.

You need his reference and he can flat out deny your request if he holds a grudge. Remember,your refusal of his offer hurt his ego.

I would suggest that you politely arrange a meeting with Prof X and talk to him in person. You are not gonna like what comes next. You are going to brown nose it. Plain and simple,there is no other way since he is in position of power and probably egoistical A-hole. Stroke his ego by telling him how much you learned from him,how you admired him and viewed him as a role model. Put together every positive experience you had while working with him and tell it in a way that it reflects good on him. Tell him how writing that letter and you getting admitted will reflect on him. BS it,embellish,but in the end,your goal here is to make Prof X happy enough to write you that letter. You don't need to grovel below him,but you need to play it tactful and smart.

I know that this sounds awful,degrading and above all else unfair,but life is unfair. Focus on the goal,bad taste goes away.

I had dealings with professors who were world class A holes with egos to the Moon and back. Asking anything from them made my stomach turn. Hell,my mentor on master thesis was like that. Superb professor,with lot of practical experience and theoretical knowledge. But he was egomaniac and a hole on the good day. But with right nudges and some ass kissing he helped me a lot. He even wrote me a letter of recommendation for my first job. Whole experience taught me thing or two how to handle those types of characters who held position of power.

Hope it helps and best of luck


You are looking for a risk-free response and there isn't one. The bottom line here is, you don't trust Prof. X, so a letter from him seems out of the question. You can be certain that this will raise eyebrows and your application may be turned down out of an abundance of caution. So let me preface my advice by saying thay this approach is not perfect. If you decide to request the letter, there's some good advice in the other responses.

1) The one thing you have going for you is the paper and your master's thesis. The master's thesis is single author, so there's no dispute as to who did what. You need to describe in your SoP precisely what your contribution to your paper was, cite the paper in the SoP, and provide a link to the paper and the thesis in case anyone cares to read it.

2) Carefully sift through the work of the professors you are targeting and describe briefly but compellingly why you would like to work in their group. Here's what will probably happen: The graduate committee will see that you are specifically mentioning a research group and will forward your application to that professor for comment. Once that happens, your SoP is in the hands of someone that can assess the quality of your work and your technical knowledge, who might actually take a look at the thesis/paper, and who suddenly has a lot of power over your application.

3) Additionally, you may want to request a letter from the senior Ph.D. student or (best) postdoc you worked most closely with; he/she should be a co-author of the work and should briefly describe in the letter in what capacity they know you before getting into the details. It should be someone you trust with keeping it confidential.

All the best.

  • José, reading between the lines in your Answer, I believe you are saying OP should not ask Prof. X for a letter. Could you confirm, or make it more explicit please, to prevent any misunderstanding? And if my understanding is correct, could you address the following: Should the OP say something in his application about the lack of a letter from the main research supervisor? If so, what should he say and where should he put it? Cover letter, a separate additional brief statement, etc.? Commented Dec 19, 2015 at 16:33
  • I would split the bounty with this answer if that were allowed. Commented Dec 20, 2015 at 15:46

I think your concern is on good grounds.

they require one of the referee must be the main research supervisor.

They normally expect a recommendation letter from Prof. X and excluding him could create a bad impression on the selection committee. Certainly the selection committee needs to know how the student worked with Prof X. Recommendation letter, the master thesis and a personal interview are more or less only logical way to reach a conclusion about the application. From my experience the recommendation letter can have the potential to influence your chances of getting admitted even if an interview gone good/bad. If you exclude Prof X, chances are that your application gets rejected in the early stage, you might even get an interview if you are lucky.

My advise is to arrange a meeting with Prof.X and openly tell him that you are applying to so and so group, you are motivated in their methods in so and so topic and explain him why you really need to be a part of them. Tell him why you turned downed his offer and honestly share your concerns. Keep in mind that this should not be an "I am sorry" type of meeting but an open discussion about what you honestly think.

Now you speculate that Prof. X would write a bad recommendation letter. I think he would have hard time in doing so if your master thesis is strong. He will have to convince the committee how bad was his experience with you, still you manage to produce a quality thesis. If you are confident about your thesis and even if you still think Prof. X would write a bad letter, I don't think it is a good idea to exclude him.

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    This is not advisable. You cannot afford a bad letter of recommendation from your research adviser. It is much more preferable not to have one. Commented Dec 17, 2015 at 13:48
  • @Prof.JoséF.Martínez they require one of the referee must be the main research supervisor stated the OP. It may be the case a bad recommendation can harm your chances but its more or less mandatory unless you are exceptional. And, the selection committee normally don't care if the student thinks that a supervisor will write him a bad recommendation, they just need one, they want to know how the student did with Prof. X from Prof. X. I have edited the answer to stress on this point.
    – Sathyam
    Commented Dec 17, 2015 at 15:06
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    "Tell him why you turned downed his offer and honestly share your concerns." Very high risk IMO. Commented Dec 17, 2015 at 16:14

You cannot afford a bad reference from your adviser(by the way, you don't have co-advisers?).

An adviser is a person who has the responsibility to supervise your work and progress. The credibility of your CV will be validated according to your adviser's recommendations, along with other professors, depending how much they were involved in your education, gaining skills, and experience.

How you can avoid all of these? I don't think "butt-kissing" as someone suggested previously is a good way. I think you should openly talk with your adviser and discuss what is their opinion about your work, progress and future prospects. Nothing neutral- everything should be solved with this conversation, since you need to decide if you want to omit his/her recommendation. After all, you would be better off having NO recommendation than a BAD recommendation.


What if you told him that working with him has made you consider a PhD, but because of family/location/other issues, you can't stay at his lab in the long term?

I mean, you're trying to get a recommendation from this professor. As much as I dislike butt-kissing on principle, it sounds like he's the sort to live on some buttering up.

I got quite a few things to work out for me by playing nice. Sometimes you have to play nice even though the other parties aren't- and I've had to play nice with some seriously malignant people. All you can do is focus on the positives of that relationship when you're talking with them, but always keep the negatives in mind. Don't get sucked into his vortex while wearing the nostalgia glasses, though. You've made a good call by not staying in his lab.

Good luck to you, OP. :)


The supervisors reference letter is one of the most important parts of your application, and for that reason I think you should try a combination of things.

For one, trying to improve the chances that your supervisor will write positive things in your letter by having a discussion with them where you outline the many positive experiences (hopefully there are some) and accomplishments from your time as a master's student. Reiterating how Prof X helped you succeed in these achievements (eg a publication) should increase the chance of these things being written in your reference letter.

As others have mentioned, you should try to explain how you had some personality conflicts with your advisor but managed to overcome these and still be successful. Mentioning that you were offered to stay as a PhD student but declined because you have a desire to learn in a new environment etc, might also help the committee see that there is something odd about the negative things written in Prof.X's reference letter.

In addition, if you are on good terms with other Prof's in the department (eg your other referee(s) or a co-advisor), or better yet the department head, it might be worth having a discussion with them about your problems as they may also be able to mention something in their reference letter that will help to outweigh any negative aspects of your supervisors letter.

All in all, a very difficult situation, but not something that should keep you from finding a PhD position if you were a successful masters student.


In this case you should not select Prof.X as your PhD guide since he behaved very badly with you. Also you should inform your fellow mates that they also don't select him as guide. My advice is that you write your master's thesis without his supervision.

He offered you a PhD position at his lab but having bad experience with him, you have done a very good job if you have politely refused by telling him that right now you don't have any plan to pursue your PhD.otherwise he (Prof. X) would have told you to write your master's thesis under him which could be disastrous for you

Since this matter is very serious you should complain about his behavior to your department's higher authorities i.e.the head,dean,chancellor,vice-chancellor,etc.

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    This answer is basically a paraphrase of the question. The part that is not just paraphrasing does not really answer the question.
    – Drecate
    Commented Dec 18, 2015 at 1:02
  • @Drecate-This may be correct my friend,but I have given a correct advice to Ray in this comment,so aparente001 should give me a bounty worth +100 reputation within 2 days and this answers the question
    – user46203
    Commented Dec 18, 2015 at 1:08
  • I removed the part that was just a copy of the question. You don't need to copy the whole question when you write an answer - just write your answer, everyone can read the question at the top of the page.
    – ff524
    Commented Dec 18, 2015 at 5:19

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