Background Tea plants belong to the genus Camellia, whose species are taxonomically complex due to frequent hybridization and polyploidy nature. The genetic genealogy of Camellia has always been a focus of botanical and ecological research, including a debate about whether Assam tea has two different domestication origins (Chinese Assam type and Indian Assam type). The chloroplast genome resources were able to provide useful data for the analysis of the plastome evolutionary relationship and species classification. Here, we determined the first chloroplast genome of the natural triploid tea plant (Camellia sinensis cv. Wuyi Narcissus) and conducted the genome comparison with Chinese type tea (Camellia sinensis var. sinensis), Chinese Assam type tea (Camellia sinensis var. assamica) and Indian Assam type tea (Camellia assamica) to improve our understanding of the evolutionary mechanism and the taxonomic classification of Camellia. Results This study presented detailed sequences and structural variations of chloroplast genomes of four tea plants. The chloroplast genome of the natural triploid tea showed no obvious sequence difference from that of other two types of Chinese teas, while that of Chinese tea and Indian tea was significant sequence difference. The natural selection probably dominated in shaping the codon bias of the chloroplast genome in tea plant, and the codon usage distribution of genome in Indian tea was obviously different from that in Chinese tea. The phylogenetic status of Chinese and Indian Assam teas was in the different branches of the tea plant. Phylogenetic tree clustering was not consistent with the current some taxonomy of Camellia. Conclusions The sequence variation of the chloroplast genome of tea plant was mainly ascribed to the expansion and contraction of the border regions (IR/ SC), which were mainly due to the sequence repeat and indel mutation events of the genome. The codon usage pattern and phylogenetic analysis supported Chinese Assam type and Indian Assam type tea might have different domestication origins and suggested the current some taxonomy of Camellia might need revision.