BackgroundThe genusRosa(Rosaceae) contains approximately 200 species, most of which have high ecological and economic values. Chloroplast genome sequences are important for studying species differentiation, phylogeny, and RNA editing.ResultsIn this study, the chloroplast genomes of threeRosaspecies,Rosa hybrida,Rosa acicularis, andRosa rubiginosa, were assembled and compared with other reportedRosachloroplast genomes. To investigate the RNA editing sites inR. hybrida(commercial rose cultivar), we mapped RNA-sequencing data to the chloroplast genome and analyzed their post-transcriptional features.Rosachloroplast genomes presented a quadripartite structure and had highly conserved gene order and gene content. We identified four mutation hotspots (ycf3-trnS, trnT-trnL, psbE-petL, andycf1) as candidate molecular markers for differentiation in theRosaspecies. Additionally, 22 chloroplast genomic fragments with a total length of 6,192 bp and > 90% sequence similarity with their counterparts were identified in the mitochondrial genome, representing 3.96% of the chloroplast genome. Phylogenetic analysis including all sections and all subgenera revealed that the earliest divergence in the chloroplast phylogeny roughly distinguished species of sectionsPimpinellifoliaeandRosaand subgeneraHulthemia. Moreover, DNA- and RNA-sequencing data revealed 19 RNA editing sites, including three synonymous and 16 nonsynonymous, in the chloroplast genome ofR. hybridathat were distributed among 13 genes.ConclusionsThe genome structure and gene content ofRosachloroplast genomes are similar across various species. Phylogenetic analysis based on theRosachloroplast genomes has high resolution. Additionally, a total of 19 RNA editing sites were validated by RNA-Seq mapping inR. hybrida. The results provide valuable information for RNA editing and evolutionary studies ofRosaand a basis for further studies on genomic breeding ofRosaspecies.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04338-0.