In order to obtain SNP markers associated with hypoxia tolerance trait for applying in molecular markerassisted breeding of Megalobrama amblycephala,in the present study,based on the constructed transcriptome data in hypoxia tolerant and sensitive M. amblycephala,52 623 potential SNPs including transition type of 30 192 (57.4%) and transversion type of 16 802 (31.9%) were found. Synonymous SNPs accounted for 99.7% of total SNPs located in the coding region,while only 32～35(0.3%) nonsynonymous SNPs were found. Five nonsynonymous and polymorphic SNPs were obtained using PCR-RFLP method. Analysis showed that two SNPs,Plin2 A1157G and Hif3α A2917G,were significantly associated with hypoxia tolerance trait in the parental populations. But further analysis revealed that no significant association existed between the two SNPs and hypoxia tolerance trait in the offspring populations. It is indicated that molecular markers isolated in the parent populations may be inappropriate in their offspring,therefore,the effectiveness of markers in offspring needs to be considered in molecular marker assisted breeding.