Your iguana can have two types of black spots on its skin. One is normal, the other is a sign of infection. The "normal" black spot is simply skin pigmentation. Other than color, it looks exactly like the green or brown scales do.

The dangerous black spots are sometimes a fungal infection called black fungus disease or black spot disease. The spots are black and differ in texture than a normal scale. They are dry, black, and crusty. It can spread and it can be contagious to another iguana, and it can make the iguana’s skin die and rot or flake off if it isn’t stopped. It is usually caused by improper habitat. If the iguana is in a dirty, wet, or moldy cage, or if it can’t get off of a dirty substance and climb to a warm and dry area, it can lead to this disease.

Some people have treated it with an antibiotic ointment (with no pain killer additive) spread thinly on the affected area, but because it might be a fungus, you may need an antifungal ointment from the veterinarian. This isn’t something that can be treated without veterinary care unless you already know what is happening. Not all black spots can be this; your iguana can get dry or wet gangrene from a bacterial infection that causes spots to turn black and die. This would also need veterinary treatment since it can also spread if it isn’t taken care of properly (sometimes you need to have the dead part of a tail or toe or spike amputated to prevent the infection from spreading). Dry gangrene makes areas turn dark/black, and it is dry and flaky. Sometimes bits break off when affected by dry gangrene. Wet gangrene is also black, but the infection makes it mushy and damp instead of dry and flaky.