Abstract: The paper aims to reveal the genetic relationship of cowpea (Vigna unguiculata) germplasm at molecular level and provide some theoretical basis for germplasm collection, identification, utilization and genetic improvement. The authors studied the genetic diversities and phylogenetic relationships of forty-one cowpea (Vigna unguiculata) germplasms from China and Malaysia based on SRAP and SSR markers. Thirtyone SRAP primers and five SSR primers with polymorphism and repeatability were selected from 65 SRAP primers and ten SSR primers for PCR amplification in 41 samples, respectively. A total of 230 bands were generated by SRAP-PCR and SSR-PCR. Thirty one SRAP primers generated 196 bands with an average of 6.3 bands per primer pair, of which 161 were polymorphic and PPB was 82.14%. Five SSR primers generated 34 bands with an average of 6.8 bands per primer pair, of which 25 were polymorphic and PPB was 73.53%. The result showed that genetic diversity of the 41 cowpea germplasms in this study was relatively rich. Cluster analysis with UPGMA method based on SRAP and SSR markers revealed that the genetic similarity among cowpea germplasms ranged from 0.1667-0.9516, and most of which were higher than 0.674. The result herein showed that 41 samples could be clearly distinguished by SRAP and SSR markers and the genetic distance among partial cowpea germplasms were high. The study will provide a reference for utilization and new variety selection of cowpea resources.