Rosa kokanica is a deciduous shrub distributed in Central Asia. We determined the genomic characteristics of the complete chloroplast genome in R. kokanica with a de novo assembly strategy. The chloroplast genome was 156,802bp in length harboring 89 protein coding genes, 37 tRNA genes and eight rRNA genes. It exhibits typical quadripartite structure comprising a large single-copy (LSC) (85,899bp), a small single-copy (SSC) (18,773bp) and a pair of inverted repeats (IRs) (26,065bp). Phylogenetic analysis of 16 chloroplast genomes from Rosaceae revealed that the genus Rosa is a monophyletic group and the R. kokanica is clustered together with the congener, R. acicular.