The complete mitochondrial genome of Crassostrea nippona was determined and compared with six other Crassostrea mitogenomes from GenBank in an attempt to shed light on the evolutionary relatedness within Crassostrea. The total length of the mitogenome was 20,030 bp for C. nippona, which was the largest among seven Crassostrea mitogenomes. Among six Asian oysters, the gene order of mitochondrial DNA was identical except for C. nippona with a transposition of trnG. While the American oyster C. virginica and Asian oysters showed broad differences in gene order with relocation of most tRNA genes and indels of duplicated tRNAs and rrnS, indicating the relatively distant relationships between the American oyster and Asian oysters. Different from other six Crassostrea oysters, C. nippona had two repeats of 66 bp in non-coding regions. Pairwise divergence among the seven Crassostrea oysters based on DNA sequences of 12 protein-coding genes ranged from 3.1 to 44.4% (Kimura two-parameter distance, K2P). The close relationship between C. nippona and C. hongkongensis was revealed by K2P of 18.9%. Phylogenetic analyses robustly revealed Crassostrea monophyly, with C. virginica at the basal position. The results of phylogenetic analyses strongly supported C. gigas and C. angulata had the closest relationship, with C. sikamea being the sister taxon. These findings presented here provide a better insight into the relationships within Crassostrea and will be useful for further evolution studies of oysters.