3 population2specific RAPD bands , namely S37 277 bp , S11 2660 bp from“Pujiang No. 1”blunt snout bream and S28 946 bp from control , were identified from the amplified bands of 100 10bp2oligo2nucleotide random primers. After gel extraction , cloning and sequencing of the 3 population2specific RAPD bands , three primers (20 base for each forward and reverse primer) were designed according to their sequence information. Then PCR amplification was carried out in the“Pujiang No. 1”and control populations. The results showed that 4 SCAR , namely Sc21 (248 bp) , Sc22 (540 bp , 460 bp) and Sc23 (320 bp) bands , were amplified by the 3 pairs of primers. Among them , Sc22 (540 bp , 460 bp) and Sc23 (320 bp) could be positively amplified in the“Pujiang No. 1”and control populations as well , but SCAR marker (Sc21 , 248 bp) developed from S37 277 bp was“Pujiang No. 1”population specificity. Large samples examination (90 individuals of “Pujiang No. 1”population , 56 individuals of control from Yuni Lake ) showed that the frequency of Sc21 marker in“Pujiang No. 1”blunt snout bream reached 91. 1 % (82/ 90) , but only 14. 3 % (8/ 56) in wild population from Yuni Lake. The high frequency of Sc21 marker in“Pujiang No. 1”blunt snout bream could be used as a specific molecular marker for population identification. And it also indicated that the frequency of some alleles related with economically important trait was increased in“Pujiang No. 1”blunt snout bream , through long2term (16 years) and high selective intensity (0. 03 % -0. 04 % selective rate) mass selection.