Abstract [Objective] To clarify the structural characteristics of the chloroplast genomes of four Anna species. in order to provide a scientific basis for its species identification and adaptive evolutionary studies in different habitats. [Methods] Chloroplast genomes were sequenced using Illumina HiSeq high-throughput sequencing. After assembly, the chloroplast genome characteristics were analyzed, and the phylogenetic tree was constructed. Adaptive evolution analysis was performed using EasyCodeML v1.21 software. [Results] Each chloroplast genomes of four Anna species had a typical tetrameric structure, with length of 154 047-154 056 bp, and encoding a total of 132-134 genes. The codon bases tend to end with two bases A and U. 173 simple sequence repeats (SSRs) were detected. The phylogenetic analysis supported that A. rubidiflora was a variety of A. ophiorrhizoides. Twelve chloroplast protein coding genes with positive selection sites were detected by adaptive evolution analysis, most of which were related to photosynthesis, fatty acid synthesis, and protein synthesis. [Conclusion] The chloroplast genome characteristics of four species of Anna were similar, and the adaptive evolution of 12 chloroplast protein coding genes might contribute to the adaptation of this species to extreme habitats such as Danxia and Karst.