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<i>Uncaria</i>, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the <i>Uncaria</i> genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four <i>Uncaria</i> species mentioned in the Chinese Pharmacopoeia and <i>Uncaria scandens</i> (an easily confused counterfeit) were sequenced and annotated. The findings demonstrated that the whole chloroplast genome of <i>Uncaria</i> genus is 153,780–155,138 bp in full length, encoding a total of 128–131 genes, containing 83–86 protein-coding genes, eight rRNAs and 37 tRNAs. These regions, which include eleven highly variable loci and 31–49 SSRs, can be used to create significant molecular markers for the <i>Uncaria</i> genus. The phylogenetic tree was constructed according to protein-coding genes and the whole chloroplast genome sequences of five <i>Uncaria</i> species using four methods. The topology of the two phylogenetic trees showed no difference. The sequences of <i>U. rhynchophylla</i> and <i>U. scandens</i> are clustered in one group, while the <i>U. hirsuta</i> and <i>U. macrophylla</i> are clustered in another group. <i>U. sessilifructus</i> is clustered together with the above two small clades. New insights on the relationship were revealed via phylogenetic research in five <i>Uncaria</i> species. This study will provide a theoretical basis for identifying <i>U. rhynchophylla</i> and its counterfeits, as well as the species of the <i>Uncaria</i> genus. This research provides the initial chloroplast genome report of <i>Uncaria</i>, contributes to elucidating the chloroplast genome evolution of <i>Uncaria</i> in China.