Black mold loves cellulose, so it usually lives on moist woody surfaces. It's possible to find it growing in your toilet bowl, however, because it's probably feeding on something else. That means your toilet must be especially dirty to sustain a black mold growth, but you probably already know that. If you get your water from a well, black stains could also come from minerals in the water, specifically iron and manganese.
The Color Black
Mold spores are everywhere, and all it takes for a colony to become established is a consistent source of moisture. The colors of mold are varied -- you can find pink, green, white or brown mold in your toilet -- but black is the most dangerous. Sensitive people can experience respiratory and skin problems when exposed to it, and people with mold allergies can have even more serious reactions. It's more common for black mold to grow on the walls and in the framing, but it will settle for a toilet, especially one in a poorly ventilated, dimly lit room that doesn't get much use.
Cleaning Black Mold
If you have black mold stains on your toilet, no one needs to tell you that it's time for a deep cleaning. You should wear a respirator and rubber gloves while cleaning it and open the window to ventilate the space. Scrub the toilet inside and out with a solution containing bleach in the proportion of 1 cup per gallon of water; use your favorite toilet bowl cleaner if it contains bleach as a disinfectant. Don't forget to scrub under the rim, inside the tank, underneath the seat, and around the base of the toilet; mold readily grows in these places. Use a clean toilet brush that you've disinfected by immersing it in solution of bleach and water.
Black Mineral Stains
You may find that some of the black stains don't come off easily with bleach; if so, they may be mineral stains. This is especially likely if you get your water from a well, because iron and manganese, which are common in groundwater, can both leave black stains. Bleach won't remove these stains, but an acidic cleanser will. One way to handle black deposits is to make a paste by mixing vinegar or lemon juice with borax, spreading it on all the blackened areas, and giving the paste several hours to work. It may take one or more repetitions, but this paste should remove the discoloration.
Deeper Cleaning and Prevention
Severe blackening from minerals may call for a stronger acidic cleanser; the strongest one you can use is muriatic acid, and even so, use it if your community allows it. This acid can burn skin and damage flooring, so handle it with gloves, goggles and plenty of respect. It works best if the water level in the bowl is low before you pour it in. Swish it around with a brush; then neutralize it with baking soda before flushing. If manganese and iron stains are a recurring problem, you may need to install a filter to remove them from your water.