Microalgae nutritional value during the larviculture has many important roles can be affected on increasing quantity and quality production. The deficiency of some fatty acids especially HUFA in formulation feed which is normally used in aquaculture, is one of the most important problem in feeding, which using the marine sources oil can solve that. In this study, standard method used in culture of two important species of microalgae in aquaculture (Nannochloropsis oculata and Isochrysis galbana) then comparative survey of their nutritional values with emphasize on DHA, EPA and ARA were done, statistically. Microalgae brought from Persian Gulf and Oman Sea Ecological Research Center- Bandar Abbas and cultured in F2 media, counted by Neobar lam and finally their fatty acids identified with Gas Chromatograph DANI-1000. Statistical analysis was done on treatments average data each with three replications by SPSS V.14( p<0.05). Fatty acid contents T- Test revealed that there are statistical differences (f=182.16, p<0.05, sig.=0.000) between two microalgae species N. oculata and I.galbana. Results showed that total FA (31.8±1.4 and 39.8 ±2.0) without any difference significantly (p>0.05), total unsaturated FA–omega 3 (9.4 ±0.5 and 30.2±0.5) , total unsaturated FA – omega 6 (19.5±0.2 and 4.7±0.6) and EPA/DHA ratio (4.38±0.6 and 0.032±0.08) with statistical difference (p<0.05) in N. oculata and I.galbana respectively.