Anisodus acutangulus (Solanaceae), an important folk medicinal herb in China, produces up to 1.2% alkaloids more than that in other Solanaceae plants such as Hyoscyamus niger, while its evolutionary position in Hyoscyameae is not very clear. Objective: To explain the evolutionary position of A. acutangulus in the Solanaceae via complete chloroplast genome(cp) sequence. Methods: Complete chloroplast genome of A. acutangulus was obtained and characterized using the Illumina PE150 pair-end sequencing data. Structure of the genome, codon usage, nucleotide variability (Pi) value, distribution of repeats and SSRs between A. acutangulus and other seven Solanaceae species were analyzed. Previously published 22 Solanaceae cp genomes were used to construct phylogenetic tree. Results: The complete cp genome of A. acutangulus is 156082 bp in length, showed the typical quadripartite structure. The complete cp genome of A. acutangulus was highly conserved. A total of 112 unique genes were found in cp genome of A. acutangulus, among which 17 were duplicated. Further, we found eight hotspot regions for genome divergence could be explored as new DNA barcodes for the identification of the Solanaceae species. Phylogenetic analysis showed that A. acutangulus formed a clade with H. niger. Conclusion: A. acutangulus belongs to Hyoscyameae subfamily and the complete cp genome provides valuable information for phylogenetic reconstruction or comparative genomics of A. acutangulus.