Abstract:In order to increase the understanding of the genetic resources of main economic loach species in China, seven microsatellite markers and mitochondrial D-Loop partial sequences were used to analyse three stocks of loach species, consisting of pond loach(Misgurnus anguillicaudatus, MA), largescale loach(Paramisgurnus dabryanus, PD), and Taiwan large loach(Uncategorized, TW).The results showed that, six microsatellite markers were commonly amplified in three stocks, whereas, one microsatellite marker(Mac239)specifically amplified in MA but failed to obtain effective amplified bands in PD and TW.Thirty-two haplotypes of D-Loop partial sequence detected in ninety individuals from three stocks were analyzed in this study, and there was only one which shared between PD and TW.A total of sixty-five variable sites were detected, twenty-nine of which were specific sites between MA and the others.It would be recently decreased of effective population size in TW, according the bottleneck and neutral test results.Based on the genetic variation analyses using microsatellite markers and D-Loop partial sequence, the closest Nei's genetic distance and K2P distance were found between TW and PD(0.297, and 0.006, respectively), obviously less than the genetic distance between MA and others(1.011-1.899, and 0.095-0.099, respectively);and the analysis of molecular variance(AMOVA)showed that extremely significant genetic differentiation among three stocks were detected in the present study(P<0.01).The results of genetic structure and haplotype network analysis suggested that relative genetic independence was showed among three stocks, whereas, similar genetic resources were only found in TW and PD.In conclusion, the distinct genetic differences in loach species would be effectively identified using molecular markers;and this paper speculated that Taiwan large loach might be the ecology stock or genetic improved population of P.dabryanus, but not effective taxonomy species.