Nannochloropsis species are known for high contents of oil or polyunsaturated fatty acids (PUFA), such as EPA (C20:5). In Nannochloropsis species, oils contain essentially saturated and mono-unsaturated fatty acids, while polar lipids are rich in PUFA. In this study, total lipids, oils and fatty acids were analyzed in 5 Nannochloropsis species. Total lipids were extracted from cells using chloroform/methanol, and from total lipids, triacylglycerols were purified using thin layer chromatography. Of the five species, four were found to be of high-oil contents and one of very low-oil content. In the high-oil species, lipids could be accumulated to more than 57% of cell dry weight at late stationary growth phase, of which triacylglycerols accounted for 32.4%–45.2% of cell dry weight. The fatty acid composition of whole cells of all five species or triacylglycerol of four high-oil content species was analyzed. In high-oil content species, saturated and mono-unsaturated fatty acids accounted for more than 95% of total fatty acids, while the polyunsaturated fatty acids were less than 5%. In contrast, in the species of low-oil content, polyunsaturated fatty acids accounted for more than 45% of total fatty acids. Triacylglycerols of the four high-oil content species possessed less than 4% PUFA and may serve as excellent raw materials for biodiesel production. On the other hand, EPA may be easily produced from total lipids of the low-oil content Nannochloropsis.