We have applied the arbitrarily primed polymerase chain reaction (AP-PCR) technique to the analysis of the relationships among six japonica and indica cultivars, and four wild species of rice. Chosen were four primers of arbitrary sequence that gave multiple amplification products when rice DNA was used as template. Among a total of 50 bands scored, 44 were polymorphic, which was sufficient to distinguish the species used in this study. It is apparent from the comparisons of genetic distances that cultivated rice (Oryza sativa) exhibits closest molecular affinity to wild O. rufipogon, suggesting that the origin of cultivated rice is from O. rufipogon. In a dendrogram of cultivated rice and O. rufipogon from different regions, japonica and indica rice were most closely clustered with O. rufipogon from China and India, respectively. Japonica and indica subspecies showed closer affinity with O. rufipogon from different origins than with each other, supporting a hypothesis of multi-centers of the origin of rice cultivation.