The aim of this study is to investigate the production of biodiesel from two kinds of microalgae Chlorella sp. and Spirulina platensis. Various items such as culture, lipid extraction and the production of biodiesel have been studied. The results showed that the rapid growth of Chlorella sp. from 0.2 to 0.5 gr per liter productivity biomass of cultivation is more suitable than Spirulina microalgae with slow growth of 0.1 to 0.3 gr per liter for the productivity biomass of culture. In comparison to 26.2% lipid content of microalgae Chlorella sp., Spirulina microalgae lipid content and the amount of 14.3 indicate a significant difference. Biodiesel output value was 28.2% by direct transesterification method. According to the results, it could be argued that microalgae Chlorella sp. features make the most suitable microalgae species for biodiesel production. These features include: rapid growth and high productivity, biomass and suitable lipid contents, environmentally easier cultivation rather than other species, suitable fatty acid profiles, having the most common fatty acids compounds (as C14:0, C16:0 and C18:0) in biodiesel. Extraction method had the best performance of extraction by the biomass Bligh and Dyer method.