In the present investigation, nine (09) unicellular microgreen algae of freshwater habitats of Manipur were characterized for total lipid content and fatty acid composition. Nile red fluorescence indicated more number of lipid bodies at stationary growth phase. Maximum lipid content was observed in Chlorella sp. (BTA-3110). Profiling of fatty acid composition showed that palmitic acid (16:0) and linolenic acid (C18:3n3) were the predominant components. Chlorococcum sp. (BTA-3112) and Korshikoviella sp. (BTA-3019) showed high palmitic acid as 54.25% and 49.68% respectively. Arachidic acid (C20:0) was maximum in Chlorella sp. (BTA-3110) as 21.57%. Among the polyunsaturated fatty acid (PUFA), linolenic acid (C18:3n3) was maximum in Chlorella sp. (BTA-3063) as 37.37%. High amount of linoleic acid (C18:2n6) was observed in Chlorella sp. (BTA-3101) as 12.62%. One of the pharmaceutically potential component, eicosapentaenoic acid (C20:5n3) occurred maximum amount in Chlorella sp. (BTA-3086). Oleic acid (C18:1n9) was the most abundant monounsaturated fatty acid (MUFA) in all the strains ranging between 0.70% to 15.79%. The levels of erucic acid (C22:1n9) and palmitoleic acid (C16:1) were also present but in low quantity in most strains. Furthermore, these potent strains which showed best lipid profile may be beneficial for use in value added products and biodiesel purpose and is appropriate for exploitation for higher scale studies.