The genetic relationship and diversity of 44 eggplants, Solanum melongena L., germplasms and 4 wild relatives were analyzed by ISSR method .One hundred and fifty-three of 186 bands were amplified by 20 ISSR primers, about 82.2% being polymorphisms. Fourty-eight germplasms were clustered into 5 groups by genetic similar index from 0.52 to 0.98, and the wild species were different from eggplants. Also 44 eggplant cultivars had a high genetic similarity and a narrow genetic diversity. At the same time, the results showed that the cluster was related to the fruit shape of eggplants and origin areas, but not to the fruit colour.