105 accessions of eggplant germplasm from China and Russia were evaluated for genetic diversity using 24 morphological traits and 25 SSR markers. Morphological variation analysis showed that 24 traits showed various degrees of diversity in all the germplasm resources, and the same trait differentiated between Russian and Chinese germplasm. Principal component analysis showed that 24 traits can be summarized as 6 factors, including fruit shape factor, the color factor, fruit appearance factor, leave shape factor, fruit calyx spines and anther stripes, and fruit characteristics accounted for the major component. Morphological traits UPGMA clustering analysis showed that the genetic similarity coefficient among those materials ranged from 0.4 to 0.8 with the mean value as 0.6. Twenty-five polymorphic SSR markers showed polymorphisms among the tested germplasm resources. A total of 122 bands were amplified using the 25 markers in 105 accessions, containing 82 alleles, among which 24.8 were effective alleles. The polymorphism information content (PIC) value ranged from 0.3 to 0.7. Molecular UPGMA clustering analysis showed that genetic similarity coefficient ranged from 0.5 to 1 with the mean value of 0.7.The clustering results obtained from morphological traits and SSR maker were similar. The clustering results of tested eggplant germplasm did not showed clear correlation to their geographic origin, but the fruit traits had some relation to clustering results.