(Bunge) Decne is the original plant species of the Chinese herbal medicine Cynanchi Atrati Radix et Rhizoma. The lack of information on the transcriptome and chloroplast genome of hinders its evolutionary and taxonomic studies. Here, the transcriptome and chloroplast genome were assembled and functionally annotated. In addition, the comparative chloroplast genome analysis was conducted between the genera and . A total of 49,801 transcripts were generated, and 20,943 unigenes were obtained from . One thousand thirty-two unigenes from were classified into 73 functional transcription factor families. The transcription factors bHLH and AP2/ERF were the most significantly abundant, indicating that they should be analyzed carefully in the ecological adaptation studies. The chloroplast genomes of and exhibited a typical quadripartite structure with highly conserved gene order and gene content. They shared an analogous codon bias pattern in which the codons of protein-coding genes had a preference for A/U endings. The natural selection pressure predominantly influenced the chloroplast genes. A total of 35 RNA editing sites were detected in the chloroplast genome by RNA sequencing (RNA-Seq) data, and one of them restored the start codon in the chloroplast of . Phylogenetic trees constructed with protein-coding genes supported the view that and were two distinct genera.