In this study, the leaves of Rutaceae species were used as materials, to extract the chloroplast DNA was extracted byusing modified CTAB method, and the chloroplast genome was sequenced by BGISEQ-500 platform, and the chloroplast genome was assembled and annotated. by BGISEQ-500 platform, Combined with NCBI database data, the whole chloroplast genome sequences of 49 species in 19 genera of Rutaceae were obtained. To clarify the phylogenetic relationships among Rutaceae and the molecular phylogenetic relationships between Zanthoxylum and its related genera after the sequence alignment, the phylogenetic trees of Rutaceae were constructed by ML and BI methods, respectively, and to provide molecular phylogenetic evidence for further exploration of the phylogenetic relationships of Zanthoxylum species. The results showed that: (1) based on the chloroplast genome sequence matrix (total length is 196 641 bp), the topological nodes of phylogenetic trees obtained by ML and BI methods were basically the same, with strong support for each branches. ，the chloroplast genome data can resolve the phylogenetic relationships of intergeneric in Rutaceae. (2) Rutaceae is a monophyletic group and further forms two branches, of which subfamily Aurantioideae is a monophyletic group and clustered with Ruta in Rutaceae into Clade I, Clade II is composed of Rutoideae and Toddalioideae, neither of which is monophyletic group. Among them, the monophyletic of Rutaceae was supported, and two major clades were formed, and within the clade I comprised an Aurantioideae lineage was sister to Ruta. Clade II consisted of Rutoideae and Toddalioideae, both of which are not monophyletic. Casimiroa and Skimmia of Toddalioideae and Dictamnus and Orixa of Rutoideae were the early-diverging clade, followed by Melicope and Acronychia. Phellodendron and Tetradium formed a clade sister to Zanthoxylum, Toddalia asiatica was nested in Zanthoxylum, and our the result supported the treatment of merging T. asiatica into Zanthoxylum. To sum up, the plastomes data were sufficiently robust to explore implications of the phylogeny for the previous phylogenetic hypotheses. The study provided a theoretical foundation for further research on the phylogenetic relationship of Zanthoxylum species level and the cultivation of new varieties.