Colorants have many applications in food, cosmetics, pharmaceutics, textile, paints, plastics, paper, ink and photographic industries. Colorants are classified according to their solubility into dyes and pigments. Those of natural origin have many advantages over synthetic ones, as natural colorants usually do not induce allergies or other health problems. In addition, their consumption in the food and drug industries is fortified with nutritional and health benefits as the majority of them possess antioxidant activity or can be used to produce some vitamins. Plants, animals, insects and microorganisms are rich sources of colorants. However, microbial pigments are favored over other natural pigments due to their higher yield, stability, economical production. Therefore, we focus in this review on fungal pigments, the history of their use, their chemistry and their applications in food and non-food fields. Additionally, the ability of the fungal genus, Epicoccum, to produce pigments is discussed. Moreover, the challenges and future prospects concerning fungal pigment production are highlighted in detail.