Abstract: Taking the pepper polyphenol oxidase family（PPOs） as the research object, the 9 codons of pepper PPO gene were analyzed by software such as CUSP,CHIPS and CodonW 1.4.4,and the codon preference characteristics of pepper PPO gene were studied, in order to provide reference for the use pattern, molecular evolution and functional exploration of the PPO gene code of pepper.The results showed that pepper PPO family genes had weak preference for codons ending in A or U（T）,including 28 high-frequency codons（RSCU＞1）,4 strong preference codons（RSCU＞1.6） and one strong preference codon（RSCU＞2）.The clustering results showed that the clustering effect based on CDS sequence was better; CaPPO1 was clustered into one group, and the other 8 genes were close.Correlation analysis showed that the main influencing factor of codon preference of PPO family genes was the GC content of codon 3 base（GC3s）.In addition,GC and C3s also have some effects.The results of ENC and neutral mapping showed that natural selection had a greater impact on the codon preference of PPO family genes.