Camellia leyeensis Chang ＆ Y. C. Zhong is a plant belonging to the genus Camellia. To determine its correct taxonomic status and better understand its molecular phylogenetic and genetic diversity, we studied the chloroplast genome of this species. Here, we report and characterize the complete chloroplast (cp) genome of C. leyeensis by using Illumina paired-end sequencing data. The chloroplast genome was determined to be 157,063 bp in length with a GC content of 37.30%. The genome contained 136 genes, including 91 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The sequence contained a large single-copy region (LSC, 86,661 bp), a small single-copy region (SSC, 18,284 bp), and two inverted repeat sequences (IRs, 26,059 bp, each). The GC content of the IR regions (42.96%) was higher than that of the SSC region (30.6%) and LSC region (35.31%). Phylogenetic analysis suggested that Camellia leyeensis is closely related to C. anlungensis with 96% bootstrap support. This chloroplast genome would be helpful for the phylogeny and conservation of Camellia.