To find the gene hypervariable regions of three varieties ofHansenia forbesiiH. Boissieu and determine their phylogenetic relationship, the chloroplast (cp) genome of these three varieties were firstly sequencing by the Illumina hiseq platform. In this study, we assembled the complete cp genome sequences ofHansenia forbesiiLQ (156,954 bp),H.forbesiiQX (157,181 bp),H.forbesiiWQ (156,975 bp). They all contained 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. The hypervariable regions between three cp genomes wereatpF-atpH,petD, andrps15-ycf1. Phylogenetic analysis showed thatH.forbesiiLQ andH.forbesiiWQ were closely related, followed byH.forbesiiQX. This study showed that the three varieties ofH.forbesiicould be identified by the complete cp genome and specific DNA barcode (trnC-GCA-petN) and provided a new idea for germplasm identification of similar cultivated varieties.