The cultivation of a species of Crassostrea in the Pearl River Delta, China, is reputed to have a ∼700-year history, the industry in Hong Kong currently being centred around the village of Lau Fau Shan in Deep Bay. The identity of the cultured species of Crassostrea in Hong Kong has been discussed for many years. The objective of this study was, therefore, to determine its specific identity by comparing the genetic distances of mitochondrial DNA sequences, that is, partial cytochrome oxidase I and 16S genes with those of other Crassostrea species. This is the first species of Ostreidae to be described genetically, in addition to shell characters. Phylogenetic analyses based on the cytochrome oxidase I and 16S data set show that Crassostrea hongkongensis is a genetically distinct taxon. The new species is genetically a sister taxon to Crassostrea nippona. Distinctive features of C. hongkongensis include an elongated, resilifer-like ligamental area, a D-shaped adductor muscle scar with a straight or slightly convex dorsal margin, three colour patterns and thin, brownish yellow lamellae covering the uneroded right valve. This study highlights the significance of using molecular genetics, accompanied by morphology, in identifying species of the notoriously phenotypically plastic Ostreidae.