Objective To resolve the controversy over the phylogenetic position of Chosenia arbutifolia in Salicaceae.

Method The whole chloroplast genome sequences of C. arbutifolia was determined by next-generation sequencing, and the phylogenetic position of C. arbutifolia was investigated by comparing its sequences with all available complete chloroplast genome sequences from the genera Populus and Salix.

Result The total genome was 155, 661 bp, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 27, 455 bp. The large single-copy (LSC) and small single-copy (SSC) regions spanned 84, 536 bp and 16, 215 bp, respectively. The total GC content of the chloroplast genome was 36.68% and 113 unique genes were annotated, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. Twenty genes were duplicated in the inverted repeat regions, 14 genes contained one intron, and three genes (rps12, clpP, and ycf3) contained two introns.

Conclusion A phylogenetic tree constructed from all available complete chloroplast genome sequences from the genera Populus and Salix based on maximum likelihood, maximum parsimony and Bayesian inference strongly supports the merging of C. arbutifolia into the genus Salix. This study would supply an important basis for the genetic study as well as conservation of C. arbutifolia.