Sequence-related amplified polymorphism (SRAP) and start condon targeted polymorphism (SCoT) molecular markers were used to detect the genetic diversity among 22 main cultivars (strains) of papaya (Carica papaya L.) in China. Genetic diversity parameters and the range of genetic similarity (GS) from SCoT were all higher than those from SRAP indicating the genetic diversity identified by SCoT was higher than that by SRAP. UPGMA cluster analysis based on combination of two molecular markers data showed that the range of GS was 0.65–0.90 among 22 papaya resources with a low genetic diversity, and all resources could be divided into three groups at the GS of 0.82. The data implied a correlation among SRAP, SCoT and these markers combination, which showed a significant relationship using Mantel test. These results indicated that the genetic basis of papaya resources in China is narrow.