Sixteen scleractinian species of six coral families (Acroporidae, Pocilloporidae, Poritidae, Faviidae, Pectiniidae, and Fungiidae) from Vietnam were analyzed for fatty acid (FA) composition. Except for the Poritidae species, total lipids of the corals had the same set of FAs, about 50% of them being unsaturated acids. Some coral families had high levels of characteristic FAs: 20:3(n-6), 20:4(n-3), and 22:6(n-3) in Pocilloporidae; 18:1(n-9) and 22:6(n-3) in Poritidae; and 18:3(n-6) and 22:5(n-3) in Faviidae. For the first time in hexacorals, unsaturated C24 FAs (24:1(n-9), 24:2(n-6), 24:2(5,9), 24:3(5,9,17), and 24:4(n-3)) were discovered in the Poritidae species. The highest level of 18:1(n-7), odd-chain and branched FAs (7.5% in total) was detected in Sandalolitha robusta. The data obtained on the contents of ten principal C18–C22 polyunsaturated FAs (PUFAs) for the 16 specimens were combined with data on the 19 reef-building coral specimens investigated previously and subjected to multidimensional scale analysis (MSA). The representative coral families (Acroporidae, Pocilloporidae, Poritidae, Faviidae, Dendrophylliidae, and Milleporidae) were separated by MSA according to the composition of their principal PUFAs. Therefore, PUFAs may serve as chemotaxonomic markers for reef-building corals at the family level. Family-specific compositions of coral zooxanthellae characterized by different PUFA profiles, which affect the PUFA content of whole coral colonies, were supposed to be the probable cause of the discovered chemotaxonomic distinctions between reef-building corals.