The clam Meretrix lamarckii is an ecologically and economically important species in the coastal regions of China. In order to characterize the genetic diversity and population structure of M. lamarckii, a 750 bp region of mitochondrial COIII gene and an 822 bp region of 12S rRNA gene were sequenced and analyzed for 118 and 105 individuals from five populations (ZS, WZ, ZP, ST and ZJ) in the Southeast coastal areas of China, respectively. Results revealed that 33 haplotypes were defined in COIII gene, and 30 haplotypes were defined in 12S rRNA gene. The pairwise Fst values between the ZS population and other four populations were range from 0.122~0.154 (COIII, P< 0.05) and 0.052~0.228 (12S rRNA, P<0.05), respectively. The revealed that ZS population was significant divergence from other four populations, and no significant genetic divergence among WZ, ZP, ST and ZJ populations. Moreover, results from the median-joining network, plot of STRUCTURE and the UPGMA trees were similar to pairwise Fstvalues. Results from AMOVA indicated that the genetic variation of M. lamarckii populations was mainly from the variation within populations (COIII: 93.27%, 12S rRNA: 92.32%). The results of neutrality tests combined with the mismatch distribution indicated recent population expansion of M. lamarckii on large spatial scales in the period of late Pleistocene (0.1-0.12 Ma).
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