Abstract: A systematic analysis of the chloroplast genome of Coffea arabica ’Bourbon’, was conducted exploring the factors affecting the formation of codon usage bias. The results indicated that the codon usage bias in the chloroplast genome of ’Bourbon’ was weak, tending towards codons ending in A/T. The ENC-GC3s plot, PR2 plot, and neutral plot analysis indicated that the preference of ’Bourbon’ codons was influenced not only by mutations but also by factors such as selection, but natural selection played a greater role. Further correspondence analysis revealed that gene expression levels, gene length, and GC content also had an impact on the bias of the ’Bourbon’ codon. The results of codon usage frequency indicated that Arabidopsis thaliana, Nicotiana tabacum, and Saccharomyces cerevisiae could be considered as expression receptor systems for the ’Bourbon’ gene, but N. tabacum and S. cerevisiae being more ideal. Study showed that 20 high-frequency codons such as GCT, TGT, GAT, etc. were discovered in Bobon coffee, and 21 optimal codons such as GCA, GCT, and TGT were determined.