Abstract: In order to clarify the characteristics and sequences variation of the chloroplast genome of Yucca,a comparative genomics of the chloroplasts was performed,and a phylogenetic tree based on the chloroplast genome was constructed. The chloroplast genome of Y. treculeana was obtained by high-throughput sequencing technology,and combined with the published chloroplast genome of Yucca,the chloroplast genomes of six species of Yucca were studied by comparative genomics,including basic structure,SSR,boundary contraction and expansion,sequence variation and phylogenetic analysis respectively. The results showed that the chloroplast genome size,gene type and number of the six Yucca species were similar,and the interspecific genome structure was conserved. Several repeated sequences were detected in the chloroplast genome of Yucca,among which SSR loci were mostly composed of mononucleotide,dinucleotide and tetranucleotide,and preferred A and T bases. Three regions with high variation（psbK-psbl-trnS-GCU,rpl20-rps12 and ccsA-ndhD）were identified from the chloroplast genomes of six Yucca species according to the nucleic acid polymorphism index（π）≥0.008. The phylogenetic relationships constructed from the chloroplast genome and LSC+SSC region sequences were basically consistent,and the phylogenetic relationships among six Yucca species were confirmed,among which Y. treculeana and Y. queretaroensis were most closely related. The sequencing obtained Y. treculeana chloroplast genome,revealed the genome characteristics and sequence variation of six Yucca species,and clarified the relatedness among various species. The results could provide reference for subsequent molecular marker development and phylogenetic research.