Abstract: 【Objective】To analyze chloroplast genome characteristics and codon preference of Yucca treculeana,so as to provide reference for the study of chloroplast-related gene expression,modification and species evolution.【Method】Chloroplast genome of Y. treculeana was sequenced,assembled and annotated to analyze codon preference and its influencing factors,and the optimal codon was screened by establishing high and low gene expression libraries. Phylogenetic tree was constructed based on 20 published chloroplast genome data of Agavaceae plants.【Result】The total length of Y. treculeana chloroplast genome was 157579 bp,and the length of the large single copy region(LSC),small single copy region(SSC),and two reverse repeat regions(IR),namely IRa and IRb regions were 85940,18279 and 26680 bp,respectively. The total GC content was 37.8%. Among 135 genes(85 protein-coding gene,38 t RNA,8 rRNA and 4 unknown functional genes),51 coding DNA sequences(CDS)with length greater than 300 bp were screened out,and the ENC was greater than 41.0. The contents of GC1,GC2,GC3 and GC3s were 46.75%,39.61%,29.19% and 26.06%,respectively,indicating that the third codon most ended in A/T. GCall was significantly correlated with GC1,GC2 and GC3(P<0.01,the same below),but GC3 was not significantly correlated with GC1 and GC2(P>0.05,the same below),suggesting that the base composition of the first and second codon of chloroplast genome was basically similar,but the similarity with the third codon was not high. Selection and mutation were the main causes of chloroplast genome codon preference. 14 optimal codons ending in A/U were screened out. Y. treculeana was sisterly with Y. queretaroensis and Y. schidigera,and the bootstrap values was 100%.【Conclusion】The chloroplast genome of Y. treculeana has a conserved tetrad structure,and the codon bias is weak,which is mainly affected by multiple factors such as selection and mutation. It is an accurate and reliable method to construct phylogenetic tree based on chloroplast genome in studying the taxonomic identification and phylogenetic relationship among plant species.