Genetic diversity of 30 local wild rice populations of Zizania latifolia collected from the Poyang Lake valley was investigated using SSR (simple sequence repeat) and ISSR (inter-simple sequence repeat) markers. A total of 253 bands were generated from 19 pairs of informative SSR primers with an average polymorphism percentage bands (PPB) of 91.67%.The average index of Nei’s genetic diversity (He) and Shannon’s information (I) were 0.2712 and 0.4144, respectively. The genetic similarity index(GS) and genetic distance (GD) ranged from 0.5590～0.8368 and 0.1632～0.4410, respectively. In comparison，with 14 informative ISSR primers, a total of 83 bands were amplified with an average PPB of 78.29%. The average He and I were 0.2386 and 0.4174, respectively. The GS and GD ranged from 0.5132～0.9342 and 0.0658～0.4868, respectively. Cluster analysis showed that 30 wild populations of Z. latifolia could be classified into three groups respectively at the threshold of 0.698 and 0.728 based on SSR and ISSR genotypes using the UPGMA analysis. There was no significant association between the phylogenetic relationship and the geographic locations in the Z. latifolia populations which might be due to human activity, water flow, animal activity, wind, etc. The results indicated that the wild populations of Z. latifolia from the Poyang Lake valley had a rich genetic diversity in SSR and ISSR genotype and thus it is of great importance to explore genetic evolution and gene resources and to preserve the local Z. latifolia populations in this area and expanded area.