Species belonging to section (Rosaceae) are mainly distributed in East Asia, and represent recently diverged lineages within the genus. Over decades, inferring phylogenetic relationships within section have been exceptional challenges, due to short branch lengths and low support values. Of approximately 36 species in the section , , and are widely distributed in the Sino-Japanese floristic region. In this study, we assembled chloroplast genomes of these three species to compare the genomic features within section , and to compare with other infrageneric groups. We found that three sect. species had lost genes with pseudogenization, and they were almost identical to each other. Two protein-coding gene regions ( and ) and five non-coding regions (5'-, --, -, - and -) were identified as being highly informative markers. Within three section chloroplast genomes, 85 simple sequence repeat (SSR) motifs were detected, of which at least 13 motifs were identified to be effective markers. The phylogenetic relationships of , and could not be resolved, even with chloroplast genome-wide data. This study reveals the chloroplast genomic data of sect. , and it provides valuable markers for DNA barcoding and phylogenetic analyses for further studies.