Relationships between chloroplast genomes (=ctDNAs) from diploid, A- genome species of rice (Oryza spp.) were established using length differences in restriction fragments of ctDNAs. Five out of 11 endonucleases used revealed differences in ctDNA fragment lengths among 19 accessions of the cultivated species, O. sativa and O. glaberrima. A larger sample of ctDNAs from 66 accessions of both wild and cultivated species were analyzed with three of those five endonucleases, resulting in the identification of nine types of chloroplast genome. In the wild species, the four geographical forms of O. perennis were found to contain one (African), one (Oceanian), three (Asian), and four (American) types, whereas O. breviligulata contained only one type of chloroplast genome. In the cultivated species, the three ecospecies of O. sativa contained one (Japonica and Javanica) and three (Indica) types, whereas O. glaberrima contained one type of chloroplast genome. The latter type was shared exclusively with O. breviligulata, suggesting that the former species had been domesticated from the latter. Two chloroplast genome types were shared by O. sativa and the Asian form of O. perennis, suggesting that the former species had derived from the latter via two domestication events.