Malus baccata(L.) Borkh. is an important wild species ofMalus. Its rich variation types and population history are not well understood. Chloroplast genome mining plays an active role in germplasm identification and genetic evolution. In this study, by assembly and annotation, six complete cp genome sequences, ranging in size from 160,083 to 160,295 bp, were obtained. The GC content of stable IR regions (42.7%) was significantly higher than that of full length (36.5%) and SC regions (LSC-34.2%, SSC-30.4%). Compared with otherMalusspecies, it was found that there were more sites of polymorphisms and hotspots of variation in LSC and SSC regions, with high variation sites includingtrnR/UCU-atpA,trnT/UGU-trnL/UAA,ndhF-rpl32andccsA-ndhD. The intraspecific and interspecific collinearity was good, and no structural rearrangement was observed. A large number of repeating elements and different boundary expansions may be involved in shaping the cp genome size. Up to 77 or 78 coding genes were annotated in the cp genomes ofM. baccata, and high frequency codons such as UUA (Leu), GCU (Ala) and AGA (Arg) were identified by relative synonymous codon usage analysis. Phylogeographic analysis showed that 12 individuals ofM. baccataclustered into three different groups with complex structure, whereas variant xiaojinensis (M.H. Cheng & N.G. Jiang) was not closely related toM. baccataevolutionarily. The phylogenetic analysis suggested that two main clades of differentM. baccatain the genusMaluswere formed and that I and II diverged about 9.7 MYA. In conclusion, through cp genome assembly and comparison, the interspecific relationships and molecular variations ofM. baccatawere further elucidated, and the results of this study provide valuable information for the phylogenetic evolution and germplasm conservation ofM. baccataandMalus.