We have developed a new method for determining ethanolamine plasmalogen contents in marine invertebrates. This quantification method involves derivatization of ethanolamine glycerophospholipid (EtnGpl) subclasses, alkenylacyl (plasmalogen), diacyl, and alkylacyl subclasses, by enzyme treatment and acetylation, followed by separation and detection by high-performance liquid chromatography (HPLC) with evaporative light-scattering detection (ELSD). This method enabled complete separation of the subclasses, and the limit of detection for plasmalogen was 200 ng (260 pmol). The peak area of plasmalogen by ELSD was unaffected by the degree of unsaturated fatty acids in EtnGpl, in contrast to ultraviolet (UV) detection. Thus, this method enables accurate determination of plasmalogen contents in various species containing marine products possessing abundant polyunsaturated fatty acids (PUFA). The method developed here was applied to marine invertebrates available in Japan. The examined marine invertebrates showed a wide range of plasmalogen contents ranging from 19 to 504 μmol/100 g wet wt. The plasmalogen levels in samples except those of class Cephalopoda and Crustacea were more than 60 mol% of EtnGpl.