The production of many currently authorized natural food colorants has a number of disadvantages, including a dependence on the supply of raw materials and variations in pigment extraction. Fungi provide a readily available alternative source of naturally derived food colorants that could easily be produced in high yields. The recent authorization of a fungal food colorant has fuelled research to explore the extraordinary chemical diversity and biodiversity of fungi for the biotechnological production of pigments as natural food colorants. These studies require an appropriate use of chemotaxonomic tools and a priori knowledge of fungal metabolites to carry out intelligent screening for known or novel colorants as lead compounds. Such screening would result in the preselection of some potential pigment producers and the deselection of pathogenic strains and toxin producers. With advances in gene technology, in the future it should be possible to employ metabolic engineering to create microbial cell factories for the production of food colorants.