The Epinephelidae is a marine fish family that has been the focus of worldwide taxonomical attention due to its economic value. Recent molecular-based phylogenies have improved understanding of species diversity within this family. Nonetheless, species misidentification or hybridization has led to a barcode index number (BIN) being associated with several species, which hampers a clear species identification within the BOLD system. In this study, grouper diversity in Vietnam was investigated to check the species inventory, provide a DNA barcode library for Vietnam, and reevaluate BINs associated with some species that are present in Vietnam. To this end, 157 specimens were barcoded corresponding to 30 species and 31 BINs. Nine species were new records, bringing to 49 the number of species inventoried for Vietnam. In BOLD, these species are associated with 75 BINs, 31 species being represented by more than one BIN. A careful review of these BINs, considering the present results from Vietnam, the species composition and frequency of each BIN in BOLD, and reference species sequences from phylogenetic studies, revealed those misidentified or hybrid specimens that artificially increased the number of BINs per species. After appropriate revision, 15 species still remained associated with more than one BIN. A phylogeographic analysis of these species demonstrated that most of the BINs derived from evolutionary lineages with geographic distributions that match well known biogeographic units in the Indo-Pacific. Beyond the species identification, these multiple BINs of each species can be used to track the biogeographic origin of each of the associated specimens.