This work is to explore the potential of producing biodiesel and valuable co-products from the biomass of Schizochytrium mangrovei PQ6 which was isolated from Phu Quoc Island, Kien Giang province, Vietnam. This microalga contains high lipid content (up to 70% of dry cell weight) and high level of total fatty adds, which is ideal for making biodiesel. The production of fatty acid methyl esters (FAME) from this marine microalga resulted in a yield of 88% based on algal oil and 44% based on algal biomass. The process of separating the obtained FAME into a first fraction enriched with saturated FAME (SFAME) and a second fraction enriched with unsaturated FAME (UFAME) was then investigated to exploit the valuable co-products. The obtained results shown that the mass fraction of SFAME and UFAME were 70% and 30%, respectively. The UFAME fraction contains a high content of DHA (accounting for 69.000% of TFAs). The test results of the SFAME fraction indicated that specific gravity at 15 degrees C, flash point, water and sediment, kinematic viscosity at 40 degrees C, sulfated ash, sulfur, copper strip corrosion at 50 degrees C, cetane number, carbon residue, iodine number, workmanship meet Vietnam Biodiesel B100 Standard. Moreover, the utilization of waste glycerol from biodiesel process as carbon source for the cultivation of the microalgae S. mangrovei PQ6 and Spirulina platensis was also investigated. (c) 2013, The Society for Biotechnology, Japan. All rights reserved.