It is a bit of an understatement to say that Abigail and John have a shared history prior to the start of Act I. It is Miller's greatness to show that some relationships, especially bad ones, between people linger around so that it is always there no matter what. Abigail and John are in that position for while much might have happened since their affair, it is there and this is what ended up transpiring between both of them. It is for this reason that Abigail seeks to conjure up a spell against Elizabeth Proctor. It is evident from early on that Abigail "will have her way, whatever it takes to get it," indicative of what she covets that Elizabeth has: Her husband. This intimation given in the first scene is forcefully conveyed in the second scene, as it is evident that both Abigail and John had an affair at one point in time. This is seen in Abigail's attempts to rekindle what was once there, only to be rejected by John who has moved on from that point. It is interesting to note that Miller brings out the idea that personal desire can be the impetus behind social and political manipulation, something that starts in the first two scenes with Abigail and will be expanded as the drama unfolds.
He had an affair (committed adultery) with her. (By the way, it's a great book. Really. If you don't plan on reading it, you should. :D)