AbstractTo assess the biodiversity of symbiotic dinoflagellates (SD) in hydrocorals, we compared the molecular species compositions of four SD lipid classes such as diacylglyceryl-3-O-carboxyhydroxymethylcholine (DGCC), digalactosyldiacylglycerol (DGDG), monogalactosyldiacylglycerol (MGDG), and sulfoquinovosyldiacylglycerol (SQDG) in Millepora dichotoma and M. platyphylla collected in shallow waters of Vietnam. A statistical analysis showed significant differences in the SD lipid composition between the hydrocoral species. These differences were influenced rather by the lipid molecules of outer membrane (DGCC and DGDG) than by the lipids of chloroplast and thylakoid membranes in SD (MGDG and SQDG). As for the fatty acid (FA) composition of lipid molecules that allow discrimination of hydrocoral SDs, the medium-chain FA 18:4 was characteristic of M. dichotoma, while the long- and very-long-chain FAs (20:5, 22:6, and 28:8) were characteristic of M. platyphylla. Thus, two different Millepora species hosted different SD groups, which had similar thylakoid lipidomes, different lipid profiles of outer membrane, and different activities in biosynthesis of n-3 polyunsaturated FAs. The lipidomic approach has shown that the M. dichotoma population is heterogenic, and about 10% of its colonies can be infected with SDs that are common for M. platyphylla.