Berchemiella wilsonii (Rhamnaceae) is an endangered endemic tree to China. Here, the chloroplast genome was characterized by next-generation Illumina paired-end sequencing. The complete genome comprised 160,076 bp in length, with an inverted repeat region of 26,514 bp, a small single copy (SSC) region of 18,717 bp, and a large single copy region of 88,331 bp. A total of 132 genes were identified, including 83 protein-coding genes, 37 transfer RNA genes, and eight rRNA genes. The overall GC content of the whole genome was 37.23%. Phylogenetic analysis showed that B. wilsonii was most closely related to Berchemiella berchemiifolia. [ABSTRACT FROM AUTHOR]