The molecular genetic variation of blunt snout bream(Megalobrama amblycephala) with different ploidy levels was investigated using 4 pairs of microsatellite primers.The results showed that:(1)In 4 primers,only 2 primers were effective,and 4-6 alleles were detected by each primer,and the size of alleles ranged from 131 bp to 307 bp.Meanwhile,two alleles(MFW19-175 and MFW19-256) were found as specific microsatellite DNA markers to distinguish allo-3n from the other four populations.(2)Shannon's diversity index,Nei's gene diversity index and the average genetic distance within each population were 0.056 2-0.288 7,0.031 5-0.196 9 and 0.039 5-0.154 2 respectively,which was a good indication of high genetic variation in five populations of blunt snout bream with different ploidy levels.(3)Both Shannon's diversity index and Nei's gene diversity index from Negative 3n hybrid,Allo-3n,Positive 3n hybrid and Auto-4n-F1 were significantly higher than those of 2n population(P<0.05).(4)Analysis of molecular variance(AMOVA) and cluster analysis indicated that there was significant divergence among five populations of blunt snout bream with different ploidy levels.The phylogenetic tree has two independent evolutionary branches.Negative 3n hybrid,Allo-3n,Positive 3n hybrid and Auto-4n-F1 shared a common group,while 2n was another independent evolutionary branch.