HELP! I have the exact same problem as the original poster, unfortunately (I don't know if this makes a difference) mine is directly over another bathroom in our basement. I can get to it from the underneath by removing the drop ceiling.
I have never done something as big as this in the DIY world and was wondering how can I when the subfloor that is rotten supports the bathroom wall. Our kitchen sink is directly behind our toilet on the opposite side of the wall and I do not want to risk the integrity of the wall. And honestly I haven't a clue if this is even do-able without taking the wall down.
It needs to be done quickly, after doing a mold test in the basement under the rotted boards we are starting to get a VERY dark mold build up, I have been spraying the boards with a bleach/mildew killer, but I know this won't help.
So after I remove the toilet... what is my next step?