A molecular genetic identification key for nine species of Crassostrea oysters was developed based on restriction fragment-length polymorphism (RFLP) analyses of nuclear and mitochondrial DNA markers. Seven of nine species were unambiguously differentiated based on digestion of the ITS-1 nuclear marker with Hae III and Hinf I. Individual species exhibited one or two RFLP patterns for each restriction endonuclease, and only C. madrasensis and C. iredalei were indistinguishable electrophoretically. All nine species were unambiguously differentiated based on digestion of the COI mitochondrial marker with Dde I and Hae III. Species exhibited one or two RFLP patterns for each restriction endonuclease, and species pairs unresolved by the first restriction enzyme were completely resolved with the second. The resulting key distinguishes among many Indo-Pacific Crassostrea oysters that overlap across some or all of their ranges, and establish as an expandable framework for future additions of other species to the key.