To provide genetic background on germplasm of blunt snout bream (Megalobrama amblycephala),SRAP (sequence-related amplified polymorphism) markers were used to investigate genetic diversity of three natural populations of M.amblycephalafrom Yuni Lake,Liangzi Lake and Poyang Lake in the middle of the Yangtze River drainage.Thirteen pairs of primer combinations,which were screened from 88 primer pairs,produced clear and polymorphic bands and were used for SRAP amplification.The numbers of amplified loci per primer pair ranged from 8 to 21,and a total of 172 loci were detected in three populations.Of which,percent of polymorphic loci (P),Nei’s gene diversity (h) and Shannon’s information index (I) were the highest in Poyang population (P =58.14%,h=0.184 9,I=0.279 9),followed by Liangzi population (P =51.16%,h=0.152 4,I=0.234 7) and Yuni population (P=29.07%,h=0.090 4,I=0.137 1).The genetic diversity was the highest in Poyang population and was the lowest in Yuni population.The Nei’s unbiased genetic distance and genetic identity among the three populations was from 0.086 6 to 0.220 7 and from 0.802 0 to 0.917 0,respectively.UPGMA cluster analysis showed that there was farther genetic relationship between the Poyang and the Yuni populations with the most genetic distance (0.220 7),and closer genetic relationship between the Poyang and the Liangzi populations with the least genetic distance (0.086 6).