Microalgae is a potential producer of functional lipids such as n-3 polyunsaturated fatty acids (PUFA) and fucoxanthin. In the present study, lipids from ten microalgae species were analyzed especially focusing on the fucoxanthin, lipid and fatty acid compositions. The study revealed a remarkable variation in total lipids content, fucoxanthin content, lipid class composition and n-3 PUFA content in individual species, although they belong to the same genus. Among microalgae examined, Pavlova lutheri contained the highest total lipids content (313.59 mg g^–1 dry weight) and considerable amount of fucoxanthin (3.13 mg g^–1 dry weight). It also had the highest level (28.01%) of total n-3 PUFA with high level of eicosapentaenoic acid (EPA) (17.76%) and docosahexaenoic acid (DHA) (7.61%). The highest fucoxanthin content (5.19 mg g^–1 dry weight) was observed in Chaetoceros gracilis. C. gracilis also contained relatively high level of total lipids (228.87 mg g^–1 dry weight) and 10.67% EPA. The results also demonstrated that Nannochloropsis oculata contained the greatest amount of EPA (26.21%), while Isochrysis galbana had the highest level of DHA (8.76%). And both microalgae contained 1.71 and 4.44 mg g^–1 dry weight fucoxanthin, respectively. Microalgal lipids containing abundant fucoxanthin and n-3 PUFA such as EPA and DHA in the present study will be used as nutraceutical lipids with great commercial potential.