Two species of rice were domesticated, Asian rice (O. sativa) and African rice (O. glaberrima). According to Londo and Chiang, O. sativa appears to have been domesticated from wild (Asian) rice, Oryza rufipogon around the foothills of the Himalayas, with O. sativa var. indica on the Indian side and O. sativa var. japonica on the Chinese and Japanese side. The different histories have led to different ecological niches for the two main types of rice. Indica are mainly lowland rices, grown mostly submerged, throughout tropical Asia, while japonica are usually cultivated in dry fields, in temperate East Asia, upland areas of Southeast Asia and high elevations in South Asia.

Current genetic analysis suggests that O. sativa would be best divided into five groups, labeled indica, aus, aromatic, temperate japonica and tropical japonica. The same analysis suggests that indica and aus are closely related, as are tropical japonica, temperate japonica, and aromatic. Further analysis of the genetic material of various types of rice indicates that japonica was the first cultivar to emerge, followed by the indica, aus, and aromatic groups, whose genome did show significant differences in age. Within the japonica group, there is some genetic evidence that temperate japonica is derived from tropical japonica.

Other studies have suggested that there are three groups of Oryza sativa cultivars: the short-grained "japonica" or "sinica" varieties, exemplified by Japanese rice; the long-grained "indica" varieties, exemplified by Basmati rice; and the broad-grained "javonica" varieties, which thrive under tropical conditions.