My boss and I have never had an easy working relationship. We disagree like crazy on most issues. We have always been able to work it out before it becomes an issue. But at times things were said that was hurtful to both of us. However when we are not disagreeing we actually work together very well. Lately however I have noticed a new trend. He's becoming more and more petty in his complaints. He blames me for this, saying that I am the one preventing the relationship from evolving. I have also been getting the feeling that he might be developing feelings that are not so collegial. It's difficult to explain why I have this feeling. Its body language, the way he looks at me sometimes, some of the things he says. Some of the things he says can easily be interpreted as flirting and if he is flirting with me then it is only now that it has become this obvious and out in the open. I should also add that he is married (I have always thought very happily so). A number of colleagues have commented on a certain chemistry between us. I have always judged it to be just two people who seem to manage to rub each other the wrong way quite often and openly. I will not deny that I find myself to be attracted to him sometimes. But I am not going to start something with a married man who is also my boss, so I have been very careful to maintain a professional distance. However, now I don't know what to expect next because sometimes he's attitude is one of barely tolerating me whilst other times he goes out of his way to make me happy. So, right now I am confused (does he like me or despise me?). I am also worried that our work relationship will not last through all this turmoil.

I don't know the answer to whether he likes you or despises you. Part of me thinks that perhaps he may be frustrated that you haven't received his advances the way he would like you to. If he is truly interested in you and you have not taken the bait, maybe that's frustrating him.

It's really hard to say and although you've provided some details, it's still hard to know the situation for all that it is.

If you are a woman with integrity and it is your virtue to not involve yourself with a married man, then continue to deal with him in a business-like manner. Don't spend any inordinate time with him alone during or afte business hours if you don't have to.

Ultimately, if he becomes outrageous or flagrant in any way, you may need to confront that behavior and he needs to know that it is not appropriate.

In my opinion, the most important part of Jakester's answer is to not spend inordinate amounts of time with him if you don't have to. Chemistry is one thing, but "forbidden" chemistry is really hard to ignore and can be misguided (in my experience). That he's married AND your boss is a double whammy. The less time you spend around him, the less it will bother you. If you keep your interactions professional then there shouldn't be any reason that the professional relationship crumbles on your end.

It might be time for a very short talk with him.
He may be attracted to you and not wanting to be, and realizing the risk both at home and at work.
But he has said nothing overt, so be careful.
You could say (privately) that perhaps it's best to keep work interactions strictly business because there are too many rumors and you like your job. That way you don't have to mention chemistry or who might be attracted to whom or not.