Background Chloroplast genome (cp genome) was once suggested as the super-barcoder to identify specific difficult organisms in the 2nd DNA barcoding conference.In 2011, the third generation sequencing platform based on the single molecule real-time (SMRT) sequencing approach was released into commercial market.With the aim of experiencing the reported advantages of the SMRT sequencing approach, we have determined the cp genome of Aconitum barbatum var.puberulum, which has the great value of clinical medication and phylogeny studies of the Ranunculaceae family.