In order to clarify the molecular mechanism of fish pharyngeal tooth development，taking Megalobrama amblycephala，a unique economic fish in China，as the research object，the cDNA sequence of secretory calciumbinding phosphoprotein （SCPP） family genes was obtained through whole genome sequence Blast. The expression of SCPP family genes in the fourth and fifth branchial arches during the critical stages of pharyngeal tooth development and in different tissues of one-year-old M. amblycephala was analyzed by qRT-PCR method to screen the key genes regulating the development of pharyngeal teeth. Multiple sequence alignment of amino acids showed that enam，scpp1，ambn，scpp9，odam，and spp1 of M. amblycephala and zebrafish share high identity，which were close to each other in the phylogenetic tree. By comparing the amino acid sequences encoded by enam and odam in different vertebrates，it was found that there were two amino acid sequence deletions in fish. The expression levels of enam，scpp1，ambn，scpp9 and spp1 in the fifth branchial arch （with pharyngeal teeth） and ribs were significantly higher than those in other tissues （P<0.05），and the expression levels of them were lowest in the fourth branchial arch （without pharyngeal teeth）. The expression levels of enam，ambn，scpp9，odam，and spp1 in the fifth branchial arch were significantly higher than those in the fourth branchial arch，and the expression level of scpp9 in the fifth branchial arch was extremely high. The results above showed that enam，scpp1，ambn，scpp9，odam，and spp1 were all involved in the regulation of pharyngeal tooth development，among which，scpp9 played a more important role in the regulation of pharyngeal tooth development，suggesting that it was more closely related to the development of pharyngeal teeth.