Aconitum brachypodum is an endangered plant endemic to south-west China. The plastid genome of this was characterized by Illumina next-generation sequencing technology. The complete plastid genome is 155,651 bp long with a pair of 26,213 bp inverted repeat regions (IRs) that are separated by a large single copy (LSC) region of 86,292 bp and a small single copy (SSC) region of 16,933 bp. A total of 132 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes and two pseudogenes. In addition, five palindromic, five forward, nine tandem repeats and 266 SSRs were detected in A. brachypodum. Furthermore, phylogenetic analysis illustrated that A. brachypodum is closely related to other ten Aconitum subgenus. Aconitum species are with high bootstrap support of 100%.