Abstract: In order to understand the genetic potential of three selective breeding populations of blunt snout bream (Megalobrama amblycephala), the genetic diversity were assessed in four populations three selective breeding populations and one foundation population (F₀) of "Pujiang No.1" selected strain of blunt snout bream on 14 polymorphic transcriptomic microsatellite loci. The parameters of genetic variabilities in three selective breeding populations are summarized as follows:the average number of alleles (A) was 7.928 6~8.785 7;the average number of effective alleles (A_E) was 4.409 4~4.878 4;the value of average observed heterozygosity (H_O) was 0.491 1~0.574 4;the value of average expected heterozygosity (H_E) was 0.741 3~0.751 8;the value of average polymorphism information content (PIC) was 0.691 2~0.705 2;the value of average Wright′s inbreeding coefficient (F_IS) was 0.229~0.352. The genetic diversity indices of A_E and H_E in three selective breeding populations were higher than those in foundation population (F₀). The LSD-t test shows that no significant difference (P>0.05) existed between foundation population (F₀) and three selective breeding populations in terms of A_E and H_E. Estimation of effective population size (N_e) for three selective breeding populations was 11.0~29.3. Recent genetic population bottleneck was detected in three selective breeding populations. The genetic distance (D_A, D_SW) among three selective breeding populations were 0.175 4~0.358 8 and 0.804 7~1.054 4, respectively. Relatively high genetic diversity and genetic potential were maintained in three selective breeding populations. Low effective population size and bottleneck effect may lead to loss of heterozygosity and inbreeding depression. Scientific measures should be taken to protect the genetic potential of selective breeding populations in the future.