The harmful effects of synthetic colorants have created an increased awareness among the stakeholders towards natural colorants, especially for applications in the fields of medicine, food and cosmetics. Such indulgence of the stakeholders has led to the exploration of natural resources like plants, bacteria, algae etc. for producing natural/organic colorants/products. Of these natural sources, microalgae are one of the valuable and recognized natural sources for producing vitamins, proteins, pigments, fuels, medicines etc.; and currently such products are gradually reaching the global markets. Microalgae produce a broad spectrum of attractive coloring pigments like chlorophylls, carotenoids, zeaxanthin, lutein, etc. These algal pigments are eco-friendly and harmless potential compounds to be applied as natural colorants in food, nutraceuticals, cosmetics and pharma industries. Producing pigments from algae has many advantages, such as, easy extraction, enhanced yields and cheaper production with no seasonal variations. This chapter discusses on the classes of algal pigments, cultivation of algae, factors affecting pigment production and metabolic engineering. In addition, the possible applications of these colorants in food, cosmetics and health care industries are highlighted too.