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The aquaculture of spotted hard clams, Meretrix petechialis, is a well‐developed industry in Taiwan. Spats have been produced for decades through artificial propagation using broodstocks selected from neighbouring culture farms on the basis of size and maturity, and the produced spats are resold to these culture farms. Although mass mortality occurs frequently in this practice, the effect of inbreeding depression has never been evaluated. Therefore, genetic diversity of 173 spotted hard clams from museums, two culture farms and three purchased populations was examined in this study. Phylogenetic analyses, based on either COI or cyt b fragments, indicated a division into lineages A and B among the samples. Cultured clams, except for one clustered with M. lusoria, museum specimens, and purchased samples from Hsinchu were all grouped into lineage A. The remaining two purchased populations were placed in both lineages. Compared with cultured clams from the Chinese coast in a previous study, our results exhibited a much lower haplotype (0.354 vs. 0.900) and nucleotide diversity (0.00113 vs. 0.00543). However, whether the loss of genetic variation is a consequence of inbreeding or the founder effect in the initial small broodstocks is unclear. The introduction of broodstocks from northern Vietnam and southern China may facilitate the management of genetic diversity. Environmental factors that potentially cause mass mortality require further investigation. [ABSTRACT FROM AUTHOR]