1. Are they completely identical? Are there any nicks on one, or are the bristled slightly worn on one? Check carefully.
2. Was the toilet filled with anything when your brush fell in? If it was empty or filled with pee, which is sterile, I would suggest microwaving it. If it was filled with poop, I'd throw em both out and throw your roommate's brush in the toilet.
I have to ask, a week ago my toothbrush fell into the toilet and I tossed it out and bought a new toothbrush naturally, that looks like my old one. Today my housemates girlfriend cleaned the bathroom and must've thought I just threw the brush out for no reason and placed it in the holder. So I go to brush my teeth, and see both brushes. WTF do I do?
My question is this... Your housemate's girlfriend fished it out of the trash and put it back?!? Yuck... That's almost certainly worse than even the toilet...
Bury them both deep in the trash can (so she can't rescue them) and buy a new one.