The acid-catalyzed transmethylation of triglyeerides and methylation of free fatty acids were achieved using methanolic HCl as reagent.The tert-butyldimethylsilylation of total fatty acids was performed with N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide after saponification of triglycerides with 5 M KOH in methanol.When combined with gas chromatography, the two methods were linear (r ≥ 0.995) with good precision and accuracy, allowing simultaneous screening analysis of fatty acids in algal lipids.The two methods were complementary of each other for the screening of microalgae containing a high content of triglycerides to be suitable for economical commercial production of biodiesel fuel.