As far as I know, recommendation letter does play significant role in admission decisions. One of my friend was denied admission for PH D just because she had a negative recommendation from her MS supervisor. The reason was almost similar; her MS supervisor wanted her to continue with her rather than going somewhere else. In her case, the MS supervisor did agree to write reco letter for her but it turned out to be negative one (she knew about it only after she was rejected for the admission on that basis). So, here are the suggestions for you. Option 1) Don't include the MS supervisor's recommendation letter in the application but do mentntion the reason why you were not able to include reco letter from your MS thesis supervisor. Please don't show negative attitude in the explanation. And, you can include your MS supervisor as one of your referees in the refree-list in your bio-data. The admission committe can contact him directly in case they want to. Note: In my case, although I had submitted a very good recommendation letter from my MS thesis supervisor, my perspective PH D supervisor had written to my master's thesis supervisor again for verification before making final decision. Option 2) Just throw a reco form in front of MS supervisor and ask him to write whatever he wants to write (even a negative reco) but do mention in your personal statement that what is the motive of your MS supervisor. (Your MS supervisor wanted you to continue at his lab but because of the wide exposure and cutting edge researches going on in US, you were inspired to go for US uni than the current one.) But you need to have very good reco letters from your UG profs and your company.