Pigments from natural sources has been obtained since long time ago, and their interest has increased due to the toxicity problems caused by those of synthetic origin. In this way the pigments from microbial sources are a good alternative. Some of more important natural pigments, are the carotenoids, flavonoids (anthocyanins) and some tetrapirroles (chloropyls, phycobilliproteins). Another group less important are the betalains and quinones. The carotenoids are molecules formed by isoprenoids units and the most important used as colorant are the alpha and beta carotene which are precursors of vitamin A, and some xantophylls as astaxanthin. The pigment more used in the industry is the beta-carotene which is obtained from some microalgae and cyanobacteria. The astaxanthin another important carotenoid is a red pigment of great commercial value, and it is used in the pharmaceutical feed and acuaculture industries. This pigments is mainly obtained from Phaffia rhodozyma and Haematococcus pluvialis and other organisms. The phycobilliproteins obtained from cyanobacteria and some group of algae, have recently been increased on the food industries. In the last years it has been used as fluorescent marker in biochemical assays. Our research group have carried out studies about the factors that improve the production of these pigments obtained from different microbial species as well as the methods for their extraction and application.