In order to reveal intraspecific variation in the tea (Camellia sinensis), the nucleotide sequence of the rbcL-accD region in the chloroplast genome of 21 Japanese tea cultivars, 22 and 7 tea clones collected in China and Vietnam, respectively, and 6 Chinese cultivars were determined. The nucleotide sequence was well conserved. Eighteen Japanese tea cultivars selected from local varieties were divided into 2 types based on 2 SNPs (Single Nucleotide Polymorphisms). One of these types (Ia) was mainly distributed in Kyoto. Both types were also found in the Asian continent, indicating that they were derived from there to Japan. Twelve additional types were found in tea of the Asian continent. Some of the tea clones from south China had one or two of the three In/Dels (insertion/deletion polymorphism), which are unique in C. taliensis and C. irrawadiensis. Chloroplast DNA can be used in order to distinguish genetic background of the cultivars of tea leaves on the market.