n‐3 Polyunsaturated fatty acids (n‐3 PUFA) from the marine microalgaIsochrysis galbana were concentrated and purified by a two‐step process—formation of urea inclusion compounds followed by preparative high‐performance liquid chromatography. These methods had been developed previously with fatty acids from cod liver oil. By the urea inclusion compounds method, a mixture that contained 94% (w/w) stearidonic (SA), eicosapentaenoic (EPA), plus docosahexaenoic (DHA) acids (4:1 urea/fatty acid ratio and 4°C crystallization final temperature) was obtained from cod liver oil fatty acids. Further purification of SA, EPA, and DHA was achieved with reverse‐phase C18 columns. These isolations were scaled up to a semi‐preparative column. A PUFA concentrate was isolated fromI. galbana with methanol/water (80:20, w/w) or ethanol/water (70:30, w/w). With methanol/water, a 96% EPA fraction with 100% yield was obtained, as well as a 94% pure DHA fraction with a 94% yield. With ethanol/water as the mobile phase, EPA and DHA fractions obtained were 92% pure with yields of 84 and 88%, respectively.