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I currently have both my bachelor's and master's degree, and have accepted admission into a doctoral program starting this September.

Most engineering doctoral programs allow you to get a master's while in the doctoral program. In my case, it only requires taking one extra class and writing a master's thesis.

What are the pros and cons of getting a second master's degree? Would it look silly on a CV to have a master's from two different institutions? If I do not complete my doctoral program, do two master's in the same discipline help with job applications at all?

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To answer the first question asked: I can't think of a single pro to having two master's degrees in the same discipline. Even if the prestige of your second school is far greater than the first, this would be strange and I would imagine it would lead anyone reading your CV to wonder exactly what it was that you were doing with your time. Note: I think it would be generally considered unethical to leave one of your master's degrees off of an academic CV. Leaving it off of a resume of some other kind might be a bit different.

A con to getting the second master's is that, as you say, you would have to write a master's thesis. Presumably you have already done this (or something similar), so doing another one could be viewed as a waste of your time.

You may likely have to enter a complete list of your degrees on various applications in your life. The only reasonable [citation needed :)] interpretation of having two identical master's degrees from different schools is that you failed to finish a PhD at the second school (because the second institution would not have admitted you into a terminal master's program for a master's degree that you already had). Not finishing a PhD is not a particularly negative thing in and of itself, but you will probably be asked to talk about why you did not finish it.

On another note, your second university may not allow you to get a second master's in the same field. You do have to fill out paperwork for these things, and the paperwork may very well ask you to list your current degrees. It's possible your application for your second master's would be denied if they realize you already have the same degree.

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It may be reasonable if they are from different schooling systems and it is not widely accepted that they are the same; your new thesis would have to be written about topics you are newly exploring at graduate school.

You might also get valuable experience through writing the new thesis if you didn't have to write anything for the first one; if this will be your first big work in the language of your new institution; or if it gives you the chance to try out working with your advisor. However, that might just mean you should write a big paper, without it officially being a thesis.

Could you get the Master's degree in a related field instead? While it would be more work, that would make you a much more versatile engineer/researcher.

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    There are some very specific Masters programmes so it would not necessarily be odd to have two Masters degrees. I have a masters in pure mathematics and another in operational research: the overlap between the two is negligible. And, what is more, I can explain why it was a good idea for me to take both. – JeremyC Mar 27 '18 at 9:38
  • @JeremyC Your situation makes sense; are both of your masters technically called "mathematics," even though one is pure math and the other is OR? I believe this question is asking about, say, 2m64 has a bachelor's degree and master's degree in civil engineering and is wondering whether to get another master's degree in civil engineering on the way to a PhD in civil engineering. – cactus_pardner Mar 27 '18 at 16:42
  • The point of my comment was that it is not at all helpful to put Masters degrees in broad categories. My pure maths masters certainly did not cover the whole subject (how could it?), and likewise my OR masters was necessarily superficial. But you only have to look at advertisements from universities for Masters programmes to see how very specific some of them are. And what about the idea of inter-disciplinary studies? – JeremyC Mar 27 '18 at 22:06
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    So the OP should avoid saying simply that all his higher degrees are in civil engineering but try to be more specific. My PhD is in statistics, but the Royal Statistical Society in the UK counts that as just one year of experience, because PhD's are very specialised. That is right: my PhD is in a very esoteric branch of statistics. The OPs masters might similarly be distinct from each other. – JeremyC Mar 27 '18 at 22:07

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