Using SRAP markers with eight primer combinations, the genetic diversity was assessed within and among seven natural populations of wild rice species in Hainan,a total of 219 alleles were detected in 120 accessions of O. rufipogon, 55 accessions of O.meyeriana and 26 accessions of O. officinalis ,and the polymorphic loci were 74.89％ , 42.47％ and 25.11％ respectively. Values obtained for Shannon's information index (I) suggested that O. rufipogon were 0.3277 showed the highest genetic diversity ，O.meyeriana were 0.2204 and O.officinalis were 0.1113 showed the lowst diversity. .UPGMA cluster analysis showed that all individuals of each population formed a distinct cluster,, that according to the geographical origin, the individuals within each population of wild rice with no cross to others. Based on the coefficient of gene differentiation, the genetic diversity of O. rufipogon groups were 0.2135, and its mean gene diversity was higher within than among populations,suggest of genetic differentiation among O. rufipogon populations was not significant, means most of the genetic diversity was due to differences within populations. Based on the results in Nei′s genetic diversity and Shannon's Information index analysis, it was suggested that populations in WDL and WDA should be given conservation priority. In addition, in situ conservation should be carried out for both O. meyeriana and O. officinalis because of a moderate genetic differentiation among populations or a small population size.