BACKGROUND: The genus Magallana represents the most commercially important oysters globally. Due to phenotypic plasticity, members of Magallana genus are often confused morphologically and therefore their taxonomical as well as conservation efforts are limited. Therefore, we aimed to sequence the complete mitochondrial genome (mitogenome) of Magallana gryphoides to explore its phylogenetic relationship. METHODS AND RESULTS: By employing the next-generation sequencing, the complete mitochondrial genome (mitogenome) of M. gryphoides was sequenced for the first time in the present study. Results suggest that the mitogenome of M. gryphoides is of 18,313 bp in length (accession number OR177662). The mitogenome contains 13 protein-coding genes including atp8 and 26 tRNAs with 3 new suppressor tRNAs as well as 2 rRNAs. The absence of rrnL splitting is unique among Crassostreinae oysters and the positions of trnG, trnV, as well as nad2 genes in the mitogenome of M. gryphoides are significantly altered. Thus, the phylogenetic analysis conducted in the present study indicates a close relationship of M. gryphoides with the native Indian oyster M. bilineata and another Asian oyster M. iredalei. CONCLUSION: Data of the present study suggest a close relationship of M. gryphoides with the native Indian oyster M. bilineata and another Asian oyster M. iredalei. These results provide a new insight into phylogenetic relationship and may help to place the correct taxonomical status of these species that are often confused in the Ostreidae taxonomy due to phenotypic plasticity.