In the study,18 pairs of primers which could give stable and polymorphic amplification profiles were screened out from 60 microsatellite loci and used to analyze the genetic structure of Parabramis and Megalobrama species.Meanwhile,the microsatellite DNA fingerprinting in six populations of genera Parabramis and Megalobrama was established based on the results of alleles of microsatellite loci by Popgen1.32 software package and illustrative patterns were constructed by EXCEL office software,including two geographic populations of M.terminalis from Dong River(SJF1)and Qiantang River(SJF2),M.hoffmanni(GDF),M.pellegrini(HHF),M.amblycephala(TTF)and P.pekinensis(CCB).The results showed that a total of 221 alleles were obtained from the six genera Parabramis and Megalobrama populations,and the alleles ranged from 2-20 in each locus.The mean value of number on alleles(N_a)of SJF1,SJF2,HHF,GDF,TTF and CCB was 5.17,6.11,3.5,6.56,5.22 and 5.22,the mean value of expected heterozygosity(H_e)was 0.634 2,0.720 4,0.546 2,0.681 0,0.675 2 and 0.559 7,and the average value of polymorphism information content(PIC)was 0.575 6,0.666 9,0.472 0,0.630 6,0.606 4 and 0.517 0,respectively.It demonstrated that the genetic diversity of SJF2 was the highest and HHF was the lowest among the six populations.Using unweighted pair-group method with arithmetic means method(UPGMA)based on their genetic distances,the cluster analysis in six populations showed that SJF2 and TTF first grouped together,genetic distance was 0.560 6;then they clustered with SJF1,GDF,HHF,CCB in sequence;the genetic distance between HHF and CCB was 1.759 2,which was the farthest.In addition,nine pairs of specific microsatellite markers(TTF1,TTF2,TTF3,TTF7,TTF10,Mam03,Mam25,EST37 and EST66)were screened from microsatellite DNA fingerprinting which could be used to identify most of genera Parabramis and Megalobrama populations.Particularly,microsatellite primers(Mam03 or EST37)could differentiate P.pekinensis(CCB)from genus Megalobrama populations and microsatellite markers(TTF3,EST37,TTF2/TTF10,EST66)combination could completely identify SJF1,HHF and GDF populations among Megalobrama spp..However,as a result of the relative consistency of the genetic characteristics,specific SSR markers,which could distinguish M.terminalis from Qiantang River(SJF2)and M.amblycephala(TTF),were not found.Overall,these results could provide a theoretical basis for germplasm conservation,species identification and genetic breeding of genera Parabramis and Megalobrama in China.