With globalization in the research trends, healthier life styles, and the growing market for the natural food colorants in the economically fast-growing countries all over the world, filamentous fungi are being investigated as readily available sources of chemically diverse colorants. With two selected examples, bioactive polyketide-Monascus-like pigments from the new fungal production strains, and the promising and yet unexplored bioactive hydroxy-anthraquinoid colorants, the present chapter highlights exciting recent findings. These may pave the way for alternative and/or additional biotechnological processes for the industrial production of natural food colorants of improved functionality. As an additional aspect, marine fungi are discussed as potential sources of novel pigments of numerous colour hues and atypical chemical structures.