Microalgae are a promising source of biofuels. However, the production of microalgal oils at a commercial scale involves high production costs, mainly associated with nutrient inputs and harvesting processes. Therefore, in order to be cost competitive, microalgae species to be used as a source of fuels should be capable of accumulating high proportions of lipids and biomass at lower fertilizer inputs and with a minimal water use impact. In the present study, mixed microalgal cultures were stablished from fresh and seawater samples. After characterizing these cultures in terms of biomass and lipid production, species were isolated from a brackish water culture that showed the best relation biomass-lipid production. Pure cultures were stablished and scaled up. A protocol for the isolation of microalgal DNA was developed and pure cultures were identified by sequencing of the small ribosomal subunit gene, using Sanger sequencing. The most productive isolate, identified as Botryococcus sp., was chosen for subsequent experiments. Botryococcus sp. was cultured under four different nitrogen and phosphorus concentrations and the effect of nutrient availability on biomass, lipid production and fatty acid composition was assessed. An increase in the relative lipid content from 25.5% under nitrogen non-limiting conditions to 41.8% under nitrogen deprivation was observed. The lipid profile induced by N limitation was found to be dominated by saturated and monounsaturated lipid classes, which meets the European Standards for biodiesel and makes oil from Botryococcus sp. suitable for biofuels production. In order to reduce the impact of microalgae cultivation in water resources, growing microalgae in wastewaters has been proposed. In this way it is also possible to remove nutrients that may cause eutrophication of waters, while producing energy. In this study, the capacity of Botryococcus sp. of removing nutrients from secondary and tertiary municipal wastewater effluents, as well as its biomass and lipid productivity under these conditions was examined. Biomass, lipid content, lipid composition and nitrogen/phosphorus removal efficiencies were measured. Results showed growth rates of 0.19 and 0.21 in the secondary and tertiary effluents, respectively and high rates of nutrient removal were observed (100%, 90% and 40% NO3-N, NO2-N and PO4-P, respectively, in the secondary effluent and 96%, 57% and 98% in the tertiary effluent). These results reinforced the possibility of using domestic wastewaters as a medium to grow microalgae. for the removal of nutrients. Moreover, high relative lipid content was found (70 - 84%) suggesting that this strain could be a good candidate for energy production. Little is known about microalgal species present in Puerto Rican waters and their diversity. Since several species belonging to Haptophyta, Chlorophyta and Bacillariophyta (diatoms) have been considered good candidates for biofuels production, getting insights into the diversity of these organisms may be important for a biofuel based project. Growing microalgae with energy purposes in the ocean has been also considered as an alternative to diminish impact on water bodies. Thus, samples of coastal waters were taken and denaturing gradient gel electrophoresis (DGGE) was conducted. Based on DGGE fingerprints, diversity and dissimilarity indices were calculated. Although similar patterns of spatial and temporal diversity between samples were observed, some of the melting types were characteristic of one site and/or sampling time. Moreover, differences between sites appear to be related to the abundance of the different melting types. Canonical correspondence analysis (CCA) showed a relation between the occurrence and abundance of the different melting types and environmental variables.