It is finding its way on to the toilet bowl surface from the air and with moisture so close is able to grow.
If the toilet is older the surface may be rough enough for it to have found its way into the porcelain enough that it will be very hard to stop now. You will have to clean the toilet more often now. Bleach will work well but how long between cleanings will be determined by how long it takes to reappear.
Try this. Turn off the shutoff under the toilet, pour a cup of bleach in the toilet tank and mix it in the water well then flush. Wait 1 hour and refill the tank with water and close the shutoff and do it again, wait 1 hour then fill and flush only with water 2 more times, no waiting, to rinse the bleach out. That will help kill any mold that may be in the water ways inside the toilet where you can't see or get at.
Get a small mirror and look under the rim of the bowl and clean out the little holes that the water comes out of also. Do this B4 you do the bleach.