The aim of this study was to construct a DNA fingerprinting database of 22 papaya major cultivars in China,and the genetic diversity was analyzed based on start condon targeted polymorphism (SCoT).The results are:(1)Effective number of alleles (Ne),Nei’s gene diversity (H) and Shannon’s information index (I) of SCoT were 1.47,0.26 and 0.39,respectively.The results indicated that SCoT markers could detect higher genetic diversity in the papaya cultivars.(2)UPGMA cluster analysis and principal coordinates analysis (PCOA) showed that the range of genetic similarity (GS) was 0.79～0.90 in most of the papaya cultivars with a low genetic diversity.All cultivars could be divided into three groups at the genetic similarity of 0.75.(3)The 22 cultivars of papaya could be absolutely identified by six SCoT primers with 99.976% probability of confidence and every cultivar of papaya had a unique fingerprint map.These results provide a beneficial reference for genetic breeding of papaya in China.