Artificial breeding of the iron clam, Cyclina sinensis, was successful for the first time in Taiwan in 2020. To prevent potential inbreeding depression and genetic incompatibility, the genetic diversity and structure of wild populations of C. sinensis must be assessed. The genetic diversity of 153 iron clams from 7 sample populations in Taiwan, including the Penghu and Kinmen Islands, was examined in this study. A total of 658 base pairs in the mitochondrial DNA cytochrome c oxidase subunit I sequence revealed only one phylogenetically informative site, and 15 haplotypes were identified. Compared with populations on the Chinese coast, those in the south of and in Taiwan Strait exhibited much lower nucleotide diversity (0.0003 vs. 0.0022), which may cause difficulties in the artificial breeding of C. sinensis in Taiwan. Compared with other bivalves, the C. sinensis of northern China did not exhibit lower nucleotide diversity (0.0022 vs. 0.002–0.006). Demographic analyses of C. sinensis in East Asia revealed no pattern of decline. Although Taiwan is closer to southern China (FST = 0.000), the introduction of broodstock from northern China should be evaluated for viability. In addition, our study revealed a difference in the genetic composition and genetic diversity of C. sinensis in Taijiang National Park before and after the enactment of the annual catch limit policy, which warrants further study.