The complete mitochondrial genome of Callista chinensis was sequenced via next-generation sequencing. The circular genome was 19,704 bp in length, containing 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a putative control region. The gene order of nad2 and nad4l was reversed when compared with that of other Veneridae species. The phylogenetic analysis indicated that the C. chinensis was clustered with Saxidomus purpurata. Comparing nucleotide sequences of the partial cox1 gene from 40 C. chinensis individuals displayed high levels of genetic diversity in the analyzed populations. Additionally, demographic history analysis based on neutrality tests and mismatch distributions suggested a recent population expansion in the C. chinensis.