SUMMARYThe total pool of coral lipids consists of lipids produced by both the coral host and its symbiotic dinoflagellates of the family Symbiodiniaceae. Betaine lipids (BL) are characteristic of plasma membranes of microalgae. Composition of such BL as 1,2‐diacylglyceryl‐3‐O‐carboxy‐(hydroxymethyl)‐choline (DGCC) that occur in coral symbionts may depend on either Symbiodiniaceae species or coral species. Membrane‐forming lipids DGCC have a zwitterion structure similar to that of phosphatidylcholine (PC). They can substitute for each other to a substantial extent, certainly in relation to membrane functions. In the present study, the profiles of DGCC and diacyl PC molecular species of symbiotic dinoflagellates from Acropora sp., Millepora platyphylla and Sinularia flexibilis were determined by high‐performance liquid chromatography with high‐resolution mass‐spectrometry. Colonies of Acropora sp. were characterized by higher contents of DGCC with eicosapentaenoic acid (20:5n‐3) and C28 polyunsaturated fatty acids; S. flexibilis, by a higher content of DGCC with palmitic acid (16:0); and M. platyphylla, by a higher content of DGCC with docosahexaenoic acid (22:6n‐3). Although the DGCC profile of the corals under study has distinctive features, it shows both similarities with and differences from the DGCC profiles of previously studied corals. Probably, each coral symbiont species has its own specific DGCC molecular species profile that is additionally modified in a certain way depending on environmental conditions created by the coral host. Molecular species DGCC and PC profiles were different. The most abundant PC molecular species were 16:0/22:5 and 38:4 in Acropora sp.; 39:5 and 38:4 in S. flexibilis; and 38:6, 16:0/22:5 and 18:0/22:6 in M. platyphylla. Thus, there is no clear evidence for any compensation or interchangeability between PC and DGCC.