The cross compatible wild relatives of cropshave furnished valuable genes for crop improvement.Understanding the genetics of these wild species mayenhance their further use in breeding. In this study,sequence variation of the nuclear Lhs1 gene was used toinvestigate the population genetic structure and gene Xowof Oryza ruWpogon and O. nivara, two wild species mostclosely related to O. sativa. The two species diverge markedlyin life history and mating system, with O. ruWpogonbeing perennial and outcrossing and O. nivara being annualand predominantly inbreeding. Based on sequence datafrom 105 plants representing 11 wild populations coveringthe entire geographic range of these wild species, wedetected signiWcantly higher nucleotide variation inO. ruWpogon than in O. nivara at both the population andspecies levels. At the population level the diversity inO. ruWpogon (Hd = 0.712; _sil = 0.0017) is 2–3 folds higherthan that in O. nivara (Hd = 0.306; _sil = 0.0005). AMOVApartitioning indicated that genetic diVerentiation amongO. nivara populations (78.2%) was much higher than thatamong O. ruWpogon populations (52.3%). The diVerentlevel of genetic diversity and contrasting population geneticstructure between O. ruWpogon and O. nivara might beexplained by their distinct life histories and mating systems.Our simulation using IM models demonstrated signiWcantgene Xow from O. nivara to O. ruWpogon,indicating a directional introgression from the annual andselWng species into the perennial and outcrossing species.The ongoing introgression has played an important role inshaping current patterns of genetic diversity of these twowild species.