Abstract:Intersimple sequence repeat (ISSR) analysis was performed in order to evaluate three successively selected populations(F7/F8/F9 of Pujiang No.1 breeding improved variety),two wild populations (Liangzi Lake/Yuni Lake of 2007)and one hatchery population (Base group, offspring of Yuni lake of 1985 ) of blunt snout bream (Megalobrama amblycephala).The sequence analysis of mitochondrial DNA cytchrome gene was also used to evaluate the effectiveness of ISSR analysis.Main results:(1)Among 100 ISSR primers,26 could produce 164 clear and repeatable bands,of which 81 bands appeared to be polymorphic(49.39%). The sequencing analysis of the cyt b gene presents that three selected generations(F7,F8,F9) of Pujiang No.1 possess the same haplotype.(2)There is a high genetic differentiation between wild/base and selected populations. Compared to Yuni Lake and base population, the percentage of polymorphic loci of F9 generation decreased by 32.34% and 30.29% respectively. Genetic distance(0.067 2),pairwise F values(0.305 72)were the highest between F9 generation and Yuni lake population. Based on the UPGMA dendrogram:the selected populations(F7,F8,F9 ) are genetically distinct they were placed in a relatively derived position as the sister branch to a branch containing wild and base populations, it also shows the closest relationship between Yuni Lake and base population. (3)The low GST value (0.141 7) combined with the high Nm value(3.027 9) contributed to lower degree of genetic divergence among selected populations (F7,F8,F9);The percentage of polymorphic loci/Average gene diversity over loci/Nei's (1973) gene diversity and Shannon genetic diversity show a tendency that it has been decreased generation by generation.(4)The ISSR technique used was confirmed to be more sensitive than cyt b sequence analysis for the study of closely related populations.(5)The authors acknowledged that,through over 20 years and 9 generations selection, compared with the wild population, Pujiang No.1 variety exhibits a significant differentiation from the wild population in genetics, and shows a rather high stability in improved trails, but there is still some distance from the plateau of selection. In the future, based on the monitoring of changes in genetic structure,potential for selection should be tapped further and attention should be paid to the possible mix in genetics, inbreeding and genetic bottleneck.