To study the association between the polymorphism of the scxa gene sequence and the intermuscular bone (IB) quantity traits,and to obtain SNPs that are significantly related to the number of IBs in Megalobrama amblycephala,the cDNA sequence of the scxa gene in M. amblycephala was obtained by cloning. Its open reading frame is 609 bp,encoding 202 amino acids. Phylogenetic analysis showed that the scxa gene of M. amblycephala is highly related with that of zebrafish,common carp,crucian carp,and golden thread carp. The fluorescence quantitative PCR results showed that the expression of scxa in the muscle and IB was significantly higher than that in other tissues,and the expression in the muscle was significantly higher than that in IB (P <0.05). By comparing the scxa exon sequence of the IB-extreme population,2 SNPs and 1 InDel that were significantly related to the number of IB were obtained. This result indicates that scxa gene plays a potential role in the development of IB,and its polymorphism is significantly correlated with the number of IB in M. amblycephala.