Ipomoea species have great economic value horticulturally, scientifically as emerging model plant system, called morning glory. Furthermore, the dried seeds of I. nil or I. purpurea used in Korean Traditional herbal medicines. In this study, we sequenced six species of Ipomoea chloroplast (cp) genomes including I. trifida, I. lacunosa, I. hederacea, and I. hederacea var. interiouscula. The six Ipomoea cp genomes were 161,354 bp to 161,750 bp in length, respectively. They have conserved quadripartite structure. A total of 112 genes comprised of 78 protein-coding regions and 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The gene order, content, and orientation of the six Ipomoea cp genomes exhibited the general structure of angiosperms and highly conserved. Comparison of the six Ipomoea cp genomes were indicated highly divergent regions and positively selected genes associated with adaptive evolution at genus Ipomoea. Phylogenetic relationships among the six Ipomoea species with 40 species based on maximum likelihood (ML) and Bayesians posterior probability (PP) was determined with other cp genomes. The six Ipomoea species are well clustered at corresponding to the APG III system of flowering classification system , respectively. In particular, I. triloba well supported in section of Batatas in this study. These results provide in useful genetic information for species identifying, taxonomy and high resolution phylogenetic relationship in the genus Ipomoea.