The systematics of oysters in the genus Saccostrea remains unclear, mainly because their taxonomy has been based on their highly variable shell forms. To obtain insights into the taxonomy of this genus, we evaluated the phylogenetic diversity of Japanese Saccostrea oysters on the basis of the nucleotide sequences of four mitochondrial genes and the ribosomal first internal transcribed spacer in the nuclear genome. Our specimens (N = 226) were divided into seven mitochondrial lineages. However, the nuclear DNA data provided strong evidence of reproductive independence for only three. For most of the lineages, it was difficult to identify a lineage-specific shell feature, thereby preventing us from establishing a decisive link between the observed lineages and morphology-based species names. Given the extreme difficulty in determining the species of Saccostrea oysters on the basis of shell morphology, we suggest that the systematics of this genus should be re-established by laying more emphasis on DNA evidence.