Extremophilic microorganisms are especially interesting from the biotechnological point of view. These microorganisms have developed mechanisms that lead to the production of valuable substances in order to survive in certain environments considered extreme for life. These substances can be used by the cosmetic, pharmaceutical industry and in human or animal feeding. Compounds obtained from extremophilic microorganisms have a great added-value since they can have unique properties and their nature can be very diverse. In this doctoral Thesis, substances such as carotenoid pigments, phycobiliproteins and carbohydrates (exopolysaccharides) are studied. Pigments are especially interesting since in recent years there has been a growing demand, by consumers, towards natural food dyes. Carotenoid pigments, and also phycobiliproteins, are of great interest for their use as feed additives, especially as color enhancers. These pigments also have great value as antioxidants and, like exopolysaccharides, have been found to display anti-cancer and anti-inflammatory activity. In addition to the currently known applications, there are microorganisms from extreme environment that are yet to be discovered and whose potential has not been studied. However, despite the biotechnological potential of extremophilic microorganisms, their use in biotechnology has certain limitations related to culture conditions, and the profitability of the compounds of interest produced. Therefore, it necessary to improve the production processes of these microorganisms in order to obtain competitive products in the market. Based on this, this Thesis had as a main objective the isolation and the study of the biotechnological potential of microorganisms from extreme environment, and improving the production strategies of target compounds, with special emphasis on reducing production costs. For this, two extremophilic microorganisms were studied: a halophilic archaea, Haloferax mediterranei and a cyanobacterium from extreme arid environment, Chroococcidiopsis sp. On the one hand, H. mediterranei stands out for its ability to produce a C50 carotenoid, particularly bacterioruberin, with high antioxidant capacity. Its possible medical application or in food industries, such as nutraceuticals, or obtaining functional foods makes bacterioruberin interesting. On the other hand, Chroococcidiopsis sp. stands out for its versatility, since it is found in very diverse extreme environments. Due to the extreme radiation that affects the rocks of the Atacama Desert, this cyanobacterium colonizes the inside of the rocks, so that the light received by a part of the endolithic colonies can be meager and diffuse irradiation. In order to be more efficient in capturing light, these cyanobacteria produce phycobiliproteins, a pigment that can be used as a food coloring and also stands out for its antioxidant capacity. Furthermore, these cyanobacteria respond to desiccation by producing a shell of exopolysaccharides, which provides a moisture environment to the cyanobacterium and has a potential use for its antibacterial and anti-inflammatory characteristics. Based on this, we optimized the growth and target metabolites production from both extremophiles. In the case of H. mediterranei, the effect of physicochemical parameters such as temperature, salinity and pH on the growth and carotenoids production was studied. In addition, the effect of nutritional factors such as glucose and yeast extract was analyzed. It allowed us to propose possible production strategies. After the isolation and identification of Chroococcidiopsis sp., the study of parameters such as the source and concentration of nitrogen or agitation was carried out to improve the cyanobacterial growth. Furthermore, the effect of other parameters such as the light irradiance on growth and the phycobiliproteins accumulation were studied. Finally, with the idea of reducing production costs, agricultural fertilizers were used as culture media, which means several advantages in large-scale cultures. The results obtained in this Thesis have contributed to improve the productivity of the biomass of these microorganisms and to the improvement in the environmental and nutritional conditions of cultivation for an optimum production of high-added value compounds. In addition, our results allow us to predict the best conditions that might contribute to address the biotechnological process on a large scale.