There has been no information on lipids of brackish water mysid Neomysis intermedia, which is the most important mysid for human food in Japan. The present study revealed their lipid content, lipid class composition, and fatty acid compositions of total lipids (TL) and major lipid classes. Lipid content of the mysid was 1.0% on wet-weight base. Major lipid classes were phosphatidylcholines (PC, 26%), phosphatidylethanolamines (PE, 24%), and phosphatidylinositols (PI, 14%), whereas the content of triacylglycerols (TAG) was relatively low (7%). Major fatty acids of the TL were 16:0 (21%), 18:1n-9 (12%), 20:5n-3 (EPA; 19%) and 22:6n-3 (DHA; 14%), and the latter two polyunsaturated fatty acids were concentrated in PI (totally 47%) and PE (43%) fractions rather than in PC (20%) and TAG (18%). Arachidonic acid (4%) was also higher in the PI (7%) and PE (5%). When the mysid was fed tri-, di- and monoacylglycerols prepared from DHA-rich fish oil, DHA mainly increased in the TAG fraction of the mysid. The mysid appeared to primarily incorporate exogenous DHA into TAG fraction.