If it's come on all of a sudden it could be that something traumatic happened. According to my vet, if there is a traumatic event one cat will often associate it with the other cat just because they were there at the time. If that's the case, the two will eventually work it out.
In my own experience, I have 3 male (neutered) cats, 2 of whom are litter mates. A few months ago, my upstairs neighbor's cat found a way to come down through a hole in their bathroom closet and ended up walking around in my drop ceiling and had to be retrieved. Strange cats falling from the sky was traumatic enough that my 2 younger cats hissed and spit at each other for a couple of weeks afterward. That was back in December and now they are fine.
Similar thing happened with a friend's 2 cats when something was knocked over onto the female while the male was in the room. It scared her and she though him responsible.