The cross compatible wild relatives of crops have furnished valuable genes for crop improvement. Understanding the genetics of these wild species may enhance their further use in breeding. In this study, sequence variation of the nuclear Lhs1 gene was used to investigate the population genetic structure and gene Xow of Oryza ruWpogon and O. nivara, two wild species most closely related to O. sativa. The two species diverge markedly in life history and mating system, with O. ruWpogon being perennial and outcrossing and O. nivara being annual and predominantly inbreeding. Based on sequence data from 105 plants representing 11 wild populations covering the entire geographic range of these wild species, we detected signiWcantly higher nucleotide variation in O. ruWpogon than in O. nivara at both the population and species levels. At the population level the diversity in O. ruWpogon (Hd = 0.712; _sil = 0.0017) is 2–3 folds higher than that in O. nivara (Hd = 0.306; _sil = 0.0005). AMOVA partitioning indicated that genetic diVerentiation among O. nivara populations (78.2%) was much higher than that among O. ruWpogon populations (52.3%). The diVerent level of genetic diversity and contrasting population genetic structure between O. ruWpogon and O. nivara might be explained by their distinct life histories and mating systems. Our simulation using IM models demonstrated signiWcant gene Xow from O. nivara to O. ruWpogon, indicating a directional introgression from the annual and selWng species into the perennial and outcrossing species. The ongoing introgression has played an important role in shaping current patterns of genetic diversity of these two wild species.