Mold

• The black stuff is likely black fungus or mold that grows in moist conditions, such as a toilet. The accumulation of substances found in human feces aids its growth in the toilet bowl, as chlorine dissipates from standing water in a toilet bowl. The high level of humidity in a bathroom also contributes to mold growth. Thoroughly and routinely cleaning the toilet with a toilet brush and bowl cleaner, especially the area beneath the bowl rim, should keep the black mold at bay.
  
  

Deteriorating Tank Components

• Another possible cause of the black stuff in a toilet is from rubber tank components that deteriorate over time or because of the effects of in-tank cleaners. A deteriorating flapper, most notably, is often the cause. Deteriorating washers on the tank-to-bowl bolts inside the tank can also occur. With gloves on, replace the flapper or other components inside the tank that may be deteriorating. Also, don't use in-tank cleaners.
  
  

Considerations

• The black mold won't just be growing inside the bowl, so be sure and clean the area between the tank and bowl and seat hinges, as well as other tight spaces on the fixture. Use a borate-based laundry detergent to clean the toilet surface.