Abstract: In this study, we investigated the genetic diversity and genetic structure of Setipinna tenuifilis populations in the Taiwan Strait and its adjacent waters. We amplified and sequenced the mitochondrial DNA control region segments by using PCR from 96 individuals of four populations(Ningde, Pingtan, Xiamen and Zhangpu). A 39-bp tandem copy was found at the 5' end of the segment and the numbers of polymorphic tandem copies were 4-7 detected in four populations. The most frequency number of copies was five in all four populations, and the number decreased from north to south. High genetic diversity was detected among the four populations, along with the high haplotype diversity and the low nucleotide diversity. We did not observe the genealogical structure corresponding to sampling locations in the neighbor-joining tree and the minimum spanning network. The gene flow and the exact P test showed that the S.tenuifilis populations in the Taiwan Strait and the adjacent waters were panmictic. AMOVA and pair-wise Fst revealed that there was no genetic differentiation or significant difference in the genetic structure between the populations. Both the mismatch distribution analysis and the neutrality tests indicated that there was a recent population expansion in S.tenuifilis, which might have occurred 25000-49000 years ago during the late Pleistocene. Despite the high genetic diversity, S.tenuifilis already showed signs of decline. More attentions should be paid on the management of fisheries in order to protect the resources of S.tenuifilis and to maintain the sustainable development.