Abstract: Neutral−plot, ENC−plot, PR2−plot and SSR epitope analysis were performed on the chloroplast genome of Rubus rufus after sequencing. The sequences of 17 Rubus plants, Geum macrophyllum voucher and G. rupestre chloroplast were aligned and the phylogenetic tree was constructed. Based on the chloroplast genome of R. rufus, the nucleotide polymorphism values among 17 plants were analyzed, and the high variable location points were screened. Finally, the shrinkage and expansion of the IR boundary region of R. rufus and 9 other species were compared by using relevant software. The findings indicated that the chloroplast genome is 156,266 bp in length, including 85,849 bp of large single copy region(LSC), 18,855 bp of small single copy region(SSC) and 25,781 bp of bidirectional repeats(IRs). A total of 129 genes were annotated, including 86 protein-coding genes, 35 tRNA genes and 8 rRNA genes. Selection pressure is the primary factor affecting codon usage preference, and all the 16 optimal codons end with A/U. The SSR of R. rufus preferred to use A and T bases. R. rufus was closely related to R. reflexus and R. cochinchinensis. The chloroplast genome sequences of 17 species of Rubus have high similarity, and the gene coding region is more conservative than the non-coding region. The variation mainly occurs in the adjacent intergenic region of the non-coding region, and the IR / SC boundary of Rubus is more conservative. The results can provide support for the classification and phylogenetic analysis of Rubus plants in the later stage.