Camellia is the largest and most important genus in the family Theaceae, with many species being of great economic, ornamental and ecological value. However, the phylogenetic resolution of these species has been difficult due to interspecific hybridization and polyploidy. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. In this study, four chloroplast genomic regions (matK, rbcL, ycf1, trnL-F) were used as markers among 161 species representing all four subgenera within this genus to investigate the phylogeny and interspecies relationship of the genus Camellia. The results showed that the 161 species of the genus Camellia could be grouped into 13 clades (A-M). Clades A and B mainly consisted of sect. Camellia. Clades C and I were made up of sect. Theopsis and sect. Eriandria. Clades D and J were composed of species from sect. Thea. Clade F consisted of the sect. Paracamellia species, whilst Clades G and M included sect. Furfuracea species. Clade H contained sect. Tuberculata and most species of sect. Pseudocamellia, whereas Clades K and L comprised the sect. Chrysantha species. These results supported that 161 Camellia species form paraphyletic groups, rather than a monophyletic group. And they demonstrated that the taxonomic position of related species could be resolved to some extent via sequencing markers in organelle genome, thus providing valuable cytoplasmic genetic information or maternal genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of various Camellia species.