Microalgae as feedstock of bioenergy, mainly biodiesel, is receiving an increased attention from scientific and industrial point of view. The selection of promising strains and optimization of the production process are essential keys to develop an economically viable project. In this context, fifty-seven strains of marine microalgae have been isolated from the Moroccan Atlantic and Mediterranean coasts. The selection of most promising strains was based on biomass productivity, lipid content and fatty acids profile. Nannochloropsis gaditana (24), Chlorella sp (67), Dunaliella tertiolecta (29), Isochrysis sp (77), Phaeodactylium tricornutum (23) and Chaetoceros sp (63) showed the best growth rate, whereas lipid content was highest in Navicula sp (up to 63%) and Tetraselmis sp (up to 56%), Dunaliella sp (up to 50%), Nannochloropsis sp (up to.60%) and Chaetoceros sp (up to 56%). Fatty Acids Methyl Ester profiles were analyzed and most strains studied showed a high rate of PUFA's mainly those belonging of Dunaliella, Tetraselmis, Isochrysis and Nannochlorpsis genuis. For Bacillariophyceae, despite their high content in lipids, their FAME profile was rich in PUFA's which affects the quality of biodiesel. This study describes the microalgae screening process and demonstrates that Nannochloropsis sp, Dunaliella tertiolecta, Isochrysis sp and Tetraselmis sp are among promising species as biodiesel feedstock. (C) 2017 Elsevier Ltd. All rights reserved.