Inter-simple sequence repeats (ISSR) were used to analyze genetic diversity and genetic structure of four cultured populations of Hydropotes inermis in four farms of Zhoushan Archipelago. Twenty-six ISSR primers yielded 286 loci in 59 individuals from the four populations. Among which 184 loci were polymorphic, and percentage of polymorphic loci (PPL) was 64.34%. Primer UBC 812 revealed the highest variation with PPL (90.91%), whereas primer UBC 860 showed the lowest variation with PPL (37.50%). Twenty-six ISSR primers were selected for the analyses of genetic diversity and genetic structure in the four population. Nei's genetic diversity (H) and Shannon's index (I) at the species level were 0.210 and 0.318, respectively. H values were between 0.1571 and 0.1895 for the four populations of Hydropotes inermis, whereas I values for the four populations were between 0.2277 and 0.2778. When comparing with the results from other animals using ISSR, the genetic diversity of the cultured Hydropotes inermis in Zhoushan Archipelago is relatively high. Among the four populations, Zhoushan (ZS) population showed the highest genetic diversity (Na=1.486, Ne=1.333, H=0.190, I=0.278, PPL=48.60%), followed by Daishan (DS) population and Xiushan (XS) population. The lowest genetic diversity was found in Zhujiajian (ZJJ) population. The analyses of population genetic structure showed that when K=4, the △K value reached maximum, which suggests that all individuals could be divided into four groups based on their genetic data. Biological data, such as skin color collected from the four populations showed that most individuals from four geographical locations could be clustered into its own group. The color of the majority of DS population was white; the color of the majority of XS population was dark grey; the color of the majority of ZJJ population was black; and the color of the majority of ZS population was light grey. These biological data indicate that there are genetic differences among the four populations studied. Furthermore, the coefficient of differentiation, Gst (0.163) obtained for the four populations with POPGENE software was similar to that obtained by AMOVA analysis (11.96% genetic variation among four populations). In order to find out genetic relationships among the four populations, Nei's genetic distance (GD) and Genetic identity (GI) were calculated. The results showed that the value of GD between ZS population and XS population was 0.045, showing that the genetic distance between these two populations is the nearest, while the value of GD was 0.066 between DS and ZJJ populations, indicating that the genetic distance between these two populations is the farthest. GI showed a similar trend to GD. The value of GI between ZS and XS populations was the highest (0.956), whereas the value of GI between DS and ZJJ populations was the lowest (0.936). Based on these results, we suggest that the increase of genetic exchange among different island populations of Hydropotes inermis, especially between ZJJ population and other three populations could improve quality traits of Hydropotes inermis. In practice, we could electronically tag the individuals of Hydropotes inermis, and systemically record the exchange information among individuals. The proposed genetic exchange could not only improve breeding for quality traits, but also scientifically and economically manage propagation of Hydropotes inermis.