Docosahexaenoic acid [DHA], an important nutraceutical, generally isolated from fish can be derived from a marine heterotroph microalgae of the thraustochytrid family. In this study, strategic screening for a high yielding strain from the mangroves of South India for the production of DHA resulted in a strain which showed promising yields of biomass and DHA. Phylogenetic (18S rRNA) analysis of this strain revealed that the isolate belonged to Thraustochytrium sp. and was labeled T01. The total lipid of the wet cell volume was detected by Nile red fluorescence spectroscopy and the lipid content was estimated by gravimetric analysis, was found to be 50 ± 2% of dry cell weight. The maximum biomass and DHA obtained using optimized (central composite design) media composition after 108 h at 25 °C and 180 rpm were 31 ± 0.2 g L−1 and 6.9 ± 0.05 g L−1 respectively. Of the total fatty acid methyl ester content in the biomass, 45.3 ± 1.7% of DHA methyl ester was observed which was improved to 80% by the urea complexation method (3.3 M urea and 3.3 Urea/FAME). This strain thus could be an ideal candidate for commercial production of DHA. © 2018 Elsevier B.V.