The spottedtail goby,Synechogobius ommaturus(Richardson)is a large,commercially important,benthic fish in the family Gobiidae,which inhabits Asian inshore waters of the Northwestern Pacific,from Japan and China to Indonesia.With the development of fishery resource,S.ommaturus is becoming an important marine food and will face higher fishing pressure.It is,therefore,very important to investigate the genetic variance and population structure of this species in order to provide the background information for the management of the species.Until now studies on S.ommaturus mainly focused on the biology and chromosome,and there are no genetic investigations for this fish.In the present study,genetic diversity of S.ommaturus and genetic differentiation between two geographical populations were analyzed.A 478 base pair(bp)fragment of the hypervariable portion of the mtDNA control region was sequenced and sequences were edited and aligned by DNA Star software.Genetic diversity indices such as number of haplotypes,polymorphic sites,transitions,transversions,indels,haplotype diversity,nucleotide diversity and the mean number of pairwise differences were obtained using the program Arlequin version 3.0.A NeighbourJoining(NJ)tree of the control region haplotypes was constructed using MEGA 3.0 and evaluated with 1 000 bootstrap replicates,and Acanthogobius flavimanus was served as the outgroup.Genetic differentiation between two populations was evaluated with the pairwise fixation index F_ST by Arlequin version 3.0.Historical demography of S.ommaturus was examined by neutrality tests and mismatch distribution analysis.The results of present study showed that haplotype diversity(0.006 3±0.003 8),nucleotide diversity(0.889 5±0.050 8)and the mean number of pairwise differences(3.000 0±1.634 3)of Dandong population were higher than those of Tianjin population.The topology of the NJ tree rooted with the outgroup A.flavimanus was shallow,and there were no significant genealogical branches or clusters corresponding to sampling localities.The pairwise fixation index F_ST (0.239 5)revealed significant genetic differentiation between these two populations.The exact test of population differentiation(non-differentiation exact Pvalues)following sequential Boferroni correction showed significant differences(P<0.01)among two populations,which rejected null hypothesis.Both mismatch distribution analysis and neutrality tests showed that S.ommaturus has experienced a recent population expansion.The observed value of the age expansion parameter(τ)was 2.508 and the time since population expansion was estimated to be 52 400-104 900 years ago.During the glacial period,with the decline in sea level,most of the Chinese continental shelf was exposed and the distribution of S.ommaturus would have been displaced to the south.These surviving individuals may have recloned north with the rise in temperature.The results suggested that the Pleistocene ice ages had a major effect on the present genetic structure of S.ommaturus. Apart from historical events,environmental factors were believed to be the important factors for shaping the contemporary phylogeographic pattern of S.ommaturus and there are some barriers to prevent gene flow between Dandong and Tianjin populations.