Abstract <p><b>Objective:</b> The molecular species of membrane lipids of the sea anemone <i>Exaiptasia diaphana</i> and the molecular species of glycolipids of its symbionts were studied. <b>Methods:</b> Lipidomic analysis was performed using high-performance liquid chromatography with mass spectrometric detection. <b>Results and Discussion:</b> A total of 82 molecular species of <i>E. diaphana</i> glycerophospholipids were identified, the main ones being 16:0/22:6 cholineglycerophospholipid (PC), 18:1e/20:4 and 18:1e/20:5 ethanolaminglycerophospholipids (PE), 18:0/22:4 serineglycerophospholipid (PS), 18:0/22:4 inositolglycerophospholipid (PI), and 18:2b/16:0 ceramidaminoethylphosphonate (CAEP). Thirty-six molecular species of glycolipids were identified in symbionts. The main molecular species were 18:4/18:5 monogalactosyldiacylglycerol (MGDG), 18:3/18:5 and 18:4/18:4 digalactosyldiacylglycerols (DGDG), and 14:0/16:0 sulfoquinovosyldiacylglycerol (SQDG). Molecular genetic analysis revealed that all <i>E. diaphana</i> colonies contained the following dinoflagellates: <i>Breviolum minutum</i>, <i>Cladocopium thermophilum</i>, and <i>Gerakladium endoclionum</i>. <b>Conclusions:</b> The profile of lipid molecular species of the coral host can act as a chemotaxonomic feature, and galactolipids of symbionts indicate resistance to changes in seawater temperature. This study contributes to the development of lipidomics of marine organisms of the phylum Cnidaria.</p>