In this work, the screening of 147 microalgal strains from the Persian Gulf and the Qeshm Island (Iran) were done in order to choose the best ones, in terms of growth (biomass) rate and lipid content for biodiesel production. A methodology, combining experiments in labscale and pilot plant (open pond) used to produce and evaluate biomass and lipid productivity is presented for the systematic investigation of the potential of different microalgae species. The culture conditions, including photo flux (180 mE m^-2 s^-1), photoperiod (12 h light/dark), temperature (25 C), pH (z8), air (carbon dioxide) and growth medium, were kept constant for all experiments. Microalgae were screened in two stages using optical density (for evaluation of biomass concentration) and Nile red and gas chromatography (for determination of lipid content and fatty acid fractions). In general, maximum specific growth rate and the maximum biomass productivity were obtained after 8e12-day culture. Nannochloropsis sp. and Neochloris sp. were selected from the marine microalgal culture collection, due to their high biomass (50 and 21.7 g L^-1, respectively) and oil content (52% and 46%, respectively). If the purpose is to produce biodiesel only from one species, Nannochloropsis sp. presented the most adequate fatty acid profile, namely linolenic and other polyunsaturated fatty acids. However, the microalgae Chlorella sp. can also be used if associated with other microalgal oils. In addition, selected strains could be potent candidates for commercial production in the open pond culture.