We found that tandem repeat (TR) arrays were present in the ark shell Scapharca broughtonii mitochondrial genome, and we demonstrated the efficiency of using this TR region as a tool for the detection of genetic differentiation. In samples collected from seven populations off the Japanese, Chinese, Russian and Korean coasts, five TR types with length ranging from 481 to 601 bp (base pairs) were found, as were 18 haplotypes (n = 155). All the Japanese samples from SD, IK, AM and KG, which represented four geographically distinct populations, had the same type of tandem repeat array, 481-TR. All the samples from China and all but one sample from Russia had the same TR type, 511-TR; these finding may be strong evidence that the ark shell populations in China and Russia are very similar. Based on a neighbor-joining dendrogram of haplotypes, the Korean population was divided into two groups as follows: samples with haplotype H481-3 and samples with haplotypes H601-1, H601-2, H601-3 or H541-1. Based on the haplotype diversity and nucleotide diversity, the Chinese, Russian and Korean populations showed a higher diversity than Japanese populations (P < 0.05).