Biodiesel production from microalgae lipids is increasingly regarded as a more sustainable and feasible alternative to conventional biodiesel feedstocks derived from terrestrial bioenergy crops. A total of ninety-six strains of marine microalgae, with an elevated biomass productivity and intracellular lipid content, were isolated from the coastal waters of Singapore using an automated flow cytometric cell-sorting technique. Cell sorting was based on the two-dimensional distribution of algal cells for red fluorescence (representing chlorophyll auto-fluorescence) against forward-light scatter (representing cell size) and red vs. green fluorescence. Twenty-one of the strains were further characterized with respect to cell growth rate, biomass concentration, lipid content (total and neutral lipid) and fatty acid profile. The growth rates of Skeletonema costatum, Chaetoceros and Thalassiosira species were greatest among the entire strains, but in terms of absolute lipid yield Nannochloropsis strains predominated. Nannochloropsis strains had a lipid content ranging from 39.4% to 44.9% of dry weight biomass. Transesterification of the lipids yielded 25-51% of fatty acid methyl ester (FAME) i.e. biodiesel, where total FAME content ranged between 11 and 21% of dry weight biomass. This study describes the microalgae screening process and demonstrates that Nannochloropsis is a promising species for biodiesel feedstock. (C) 2011 Elsevier Ltd. All rights reserved.