What causes pigmentation in moulds?

Answer 1

For a journal article about this, see http://jds.fass.org/cgi/content/full/85/11/2786

Pigmentation can be attributed to many factors. Mold hyphae are often colorless, but the fruiting bodies (reproductive structures) are often pigmented. If you let a piece of bread or orange peel mold, you can often see the colors blue, white and black.

Hope that helps.