Can I apply for PhD without recommendation from my masters advisor? I am currently applying for a PhD in a very competitive top tier university, which requires three references. I have two referees (my tutor and my undergraduate research project supervisor) who I am quite sure would write very good references for me. 

I am stuck with the choice of my third referee: 

I am currently doing a masters, but my masters supervisor is overly precise and temperamental. Although he is the "ideal" choice as my referee as he can comment on my research capabilities and working in a laboratory environment, I am certain that his reference will be lukewarm or may even be negative as I am currently having difficulty getting along with him. (ADDITION: I had only worked with this supervisor for 2-3 months. I also had an undergraduate research project supervisor who can also comment on my research abilities).   

Alternatively, I have asked one of my lecturers (who I get along with very well) in my undergraduate, and he is very happy and eager to write a reference for me. I am quite sure that he will write a positive reference in support of my application. But he is unable to comment on my research abilities (just my academic capability and personality). Additionally, wouldn't the admissions tutors suspect that something is going on if all my referees are undergraduate even when I am taking a master's course??

What should I do?

PS. The problem is that he initially offered me a PhD position despite the fact that I wanted to pursue and applied for a masters programme. I turned it down as I was not interested in the PhD project and when I told him about my applications to other, top tier universities, his attitude towards me has changed and became very impatient, frustrated and uninterested. This is the reason why I am quite certain he will not be writing a positive reference for me.
Can I apply for PhD without recommendation from my masters advisor?


Yes, you can apply, but you may experience great difficulty in getting accepted. 


  Additionally, wouldn't the admissions tutors suspect that something is going on if all my referees are undergraduate even when I am taking a master's course??


Most likely, yes.


  I am certain that his reference will be lukewarm or may even be negative as I am currently having difficulty getting along with him.


As others have suggested, the very important first step is to ask your advisor for a strong recommendation letter. If he agrees, no problem. If not, and there is nobody else that can comment in a strong, positive way about your research capabilities/potential, you may need to take a break from your studies and come up with a plan about how to move forward. I have been in such a situation.

I had a falling out with my MS advisor. I knew that he wouldn't write me a strong letter (I was not on speaking terms with him and I can't say much more than that). I also knew that I would need several strong recommendation letters commenting on my research capabilities/potential to continue on with my goal of pursuing a PhD. To get strong recommendations, I decided to go back into industry for a few years. In my field, a good percentage of industry jobs that I qualified for are heavily R&amp;D focused. A good couple of years back in that environment landed me some solid opportunities to work on some cool stuff and impress some people who were very willing to help me out with pursuing my long-term goals. 

I'd like to point out that this is still not a fail-safe approach: several schools I applied to explicitly asked me to submit a recommendation from my MS advisor. I explained to them my circumstance (it's actually a pretty good story), but that did not matter to them. I was very fortunate that one of my industry-based references was considered a big shot by several top schools I applied to, and for those schools that did not ask for a reference from my MS advisor, that worked out well for me. While there was a lot of hard work that went into my plan, I also feel in some ways that I got very lucky.

So, if you cannot get a strong recommendation from your MS advisor, be prepared to take some relatively drastic measures to improve your chances of success. Also, if it is possible in your field of study, leverage the skills you have obtained to build up some strong research references.