Objective To investigate the chloroplast genome phylogeny, codon usage bias patterns and the influence factors of medicinal plants in the genus Elsholtzia. Methods The MISA, IRSCOPE, and mVISTA software was used to analyse chloroplast genome characteristics of 5 plants in the genus Elsholtzia. Using CodonW 1.4.2 software, CUSP, chiplot, and MEGA for codon bias and phylogenetic analysis. Results The coding regions of the chloroplast genomes of five species of Elsholtzia are highly conserved, and the boundaries of the chloroplast genomes are relatively stable, with small variations in the chloroplast genomes. The average GC content (GCall) of the coding region of the chloroplast genomes in the 5 Elsholtzia plants was less than 40%, indicating that codons prefer to use base A/U, the optimal codon shared by 5 plant species is AAU; the number of effective codons (ENC) in the chloroplast genomes of 5 plant species ranges from 35.88 to 61.00, indicating weak codon preference, combining ENC plot analysis, neutral plot analysis and PR2-plot analysis, it can be concluded that the five species chloroplast genomes codon preferences are influenced by natural selection and mutations, among which natural selection plays a dominant role. The results of phylogenetic analysis show that the closest genetic relationship is between Elsholtzia splendens and Elsholtzia rugulosa. Conclusion This study laid the foundation for the genetic structure and diversity research of Elsholtzia plants, and provided a certain theoretical basis for chloroplast genetic engineering and improvement of exogenous genes.