Oyster aquaculture is a new and fast growing sector in Vietnam, but confusion exists about the identity of the species presently under culture, whether they are Pacific oysters (Crassostrea gigas), Portuguese oysters (Crassostrea angulata), hybrids thereof, or other species. This study was carried out to identify which oyster or oysters are most commonly cultured in Vietnam and, additionally, once the species identity was resolved, to assess three farmed Vietnamese stocks for levels of genetic variation and suitability for captive breeding programs. To resolve the taxonomy issues, we searched for nucleotide differences (characteristic attributes) in published mitochondrial DNA cytochrome c oxidase subunit 1 (COI) sequences that, for the first time, would categorically separate and distinguish in particular C. angulata from C. gigas. On review of 300 published haplotypes of C. angulata and C. gigas based on a 293 bp nucleotide-fragment of published COI sequences, we found that there were five distinct nucleotides that are categorically different between C. angulata and C. gigas and that could be considered as diagnostic nucleotides. Using these five diagnostic nucleotides, we confirmed that the samples from northern Vietnam are C. angulatam, not C. gigas. Similarly, we identified other oyster species in Vietnam from Nhatrang as C. sikamea and C. madrasensis. DNA microsatellite data (following) can also support understanding of the taxonomy, directly by comparing allele types and frequencies between putative species, but also indirectly because as nuclear DNA, microsatellite genotypes may reveal if hybridization is occurring (as evidenced by deviations from Hardy-Weinberg equilibrium). No evidence, considering Hardy-Weinberg deviations, for interspecific hybridization was found. To address the diversity issues, three hatchery bred populations of C. angulata were screened for allelic variation at nine DNA microsatellite loci. All three lines had high allelic diversity, moderate effective population sizes (Ne), and little evidence of kinship, which, by precent with other hatchery bred highly fecund oyster species, is a little unexpected. It is speculated that local hatchery practises may involve sharing stock among hatcheries which then may contribute to the maintenance of moderate to high levels of diversity during hatchery reproduction of this highly fecund species.