Microalgae are a promising alternative source to produce biofuels and bio-products, as they consume carbon dioxide to grow, multiply quickly, and can be cultivated in domestic and industrial wastewater. The efficiency of microalgae-based biodiesel industry depends on the selection of appropriate strains with best lipid content yields and adequate fatty acids composition. The aim of this study was to select a potential microalga strain for lipid production by bioprospecting and screening lipid productivity and fatty acid compositions of some local microalgae isolated from different water bodies located in the region of Agadir, Morocco and cultivated in homemade photobioreactors. For this purpose, four freshwater microalgae Parachlorella kessleri, Cyclotella species, Chlorella species and Closterium species were isolated and cultivated. Lipid extraction was carried out using Soxhlet and fatty acids profiling was performed using Gas Chromatography. The highest lipid content was obtained with a diatom microalga Cyclotella spp. (33 wt%) after 15 days of residence time. The investigated strains produced high amount of oleic acid (41-54%) followed by linoleic (18-33%), palmitic (13-23%) and stearic acid (4-12%), respectively. Variations in lipid production and fatty acids composition as responses to changes in residence times form another important factor to feedstock selection for biofuel production. Key words: Biofuel, biomass, culture time, fatty acid, freshwater microalgae, lipid.