Abstract: In order to explore the functional structure of chloroplast genome and the codon usage preference of the tea Camellia rubituberculata, 57 protein coding sequences were screened by CodonW, CUSP and CHIP, and then analyzed by neutral mapping, ENC-plot and PR 2-plot. The results showed that the total length of chloroplast genome was 157 044 bp, showing a four-segment structure, and the sequence was GenBank（MN 913340）. A total of 136 genes were obtained, including 83 protein-coding genes, 45 tRNA genes and 8 rRNA genes. The average content of GC was 38.04%, and the number of effective codons ranged from 35.64 to 56.67, with an average value of 46.44, indicating weak codon bias. Among 32 codons with RSCU＞1, 28 codons ended in A or U, indicating that the chloroplast genome preferred to use codons ending in A or U. The results of neutral plot analysis, ENC-plot analysis and PR 2-plot bias analysis all proved that natural selection was an important factor influencing codon bias, and 12 optimal codons（UUG, UCU, UCC, UCA, CCC, CCA, ACC, ACA, AGG, GAU, GGA, AUA） were screened. This study provided relevant data support for studying the phylogeny of Camellia plant at the molecular level.