The aims of this study were to clarify the intra- and inter-specific chloroplast DNA (cpDNA) variation in the genus Camellia and to assess its evolutionary process in Japan. Sequencing or PCR-RFLP analyses were performed at two cpDNA regions, atpH-atpI and trnL-trnF. Three haplotypes (Haplotypes Ia, Ib and III) were found in C. japonica and there was a distinct geographical distribution pattern in the haplotypes of this species in Japan. Haplotypes Ib and III, which characterised C. japonica, were not detected in Chinese Camellia. We conclude that mutations of cpDNA in C. japonica might have originated in Japan, especially in the islands of western Kyushu and that these genetically rich areas are probably the glacial refugia of C. japonica. The evolutional history of the genus Camellia is also discussed.