Sex-specific DNA markers are useful for studying sex-determination mechanisms and establishment of monosex populations. Three widely spaced geographical populations (Liangzi, Poyang and Yuni Lakes in China) of blunt snout bream (Megalobrama amblycephala) were screened with AFLPs to search for sex-linked markers. Female and male pools (10 individuals in each pool) from each population were screened using 64 different primer combinations. A total of 4789 genomic fragments were produced, with a mean frequency of 75 bands per primer pair. Three different primer combinations produced putative sex-associated amplifications and were selected for individual screening in the three populations. However, none showed sex specificity when we converted these three markers into sequence characterized amplified region markers and evaluated all the individuals from the three populations.