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Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of O. sativa and its close relatives (Oryza rufipogon and Oryza nivara), we investigated nucleotide diversity data from 10 unlinked nuclear loci in species-wide samples of these species. The results indicated that O. rufipogon and O. nivara possessed comparable levels of nucleotide variation (θ_sil = 0.0077∼0.0095) compared with the relatives of other crops. In contrast, nucleotide diversity of O. sativa was as low as θ_sil = 0.0024 and even lower (θ_sil = 0.0021 for indica and 0.0011 for japonica), if we …