Looking for a Ph D, should I write them that I am wheelchair user from the first time?

My accident happened during univ time, so my marks were very low for those years. However, then, I improved my marks and I also finished a MSc very good. Should I tell them that the situation was because of my accident?

Whilst poor performance during a first degree can have many perfectly valid causes, it will be the opinion of many of the people you apply to that this should have been taken into account when your degree was awarded and your mark adjusted accordingly. Therefore I would not suggest stressing the point too much. If you got a 2(i) in your first degree I wouldn't even bother mentioning that you faced extenuating circumstances.

It's a judgement call as to whether you should mention that you are a wheelchair user in your first contact to the supervisor. If you are asked, you should certainly volunteer the information. If not, it may be better to commit somebody to interviewing you before they start thinking about how long it'll take to have the lab refitted to accommodate a wheelchair properly.

You'll certainly need to mention that you're a wheelchair user if you need to arrange an interview - access to many university buildings (particularly older one) is not always what it should be. You are much less likely to encounter discrimination once you've got this far.