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I am currently in the process of looking for a phd position (in math). Almost all universities require three recommendation letters (some only require two, but ideally I'd have three) from professors. The problem is that I went through my studies rather anonymously and don't really know anyone. For one of these letters I am going to ask the advisor of master thesis which seems like a pretty clear choice with no real reason against it.

Possible options for the others would be:

-The professor who held the seminar I was in last semester. I got an A+ on my talk and he probably has more to say about me than someone whos lecture I was in.

-The advisor of my bachelor thesis. The thesis was apparently considered very good in terms of mathematical content, but a bit flawed as there were quite a few small mistakes left (typos etc.). I also got very good grades in all of her exams. Reasons against her would be that the Bachelor thesis was in a different area of mathematics, I haven't talked to her for 2 years and that the accompanying seminar talk of my Bachelor thesis was rather mediocre.

-Any other professor in whose exam I had a good grade. There would be a few candidates, but besides from the oral exam I never really talked to them.

Another point mentioning is that I have excellent grades, so I guess that these letters are supposed to focus a bit more on soft skills (communication etc.)?

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I would put this as a comment, but I'm under 50 reputation, so here goes.

The first three professors you mentioned sound like your best bet. Thesis advisors can vouch for your ability to do mathematical research, which is the primary skill that phd programs are looking for.

It is not uncommon for people to ask professors who they only had for a class, though letters that say no more than "did well in class" are not very impactful. It is better if the professor oversaw some extended class project, or even better, a thesis. Remember, the phd admissions committees want students who are motivated and capable of doing research, not just doing well in the classroom.

EDIT: Additionally, I would not worry about the fact you have not kept in contact with your undergraduate thesis advisor. This is surely a common scenario.

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