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<i>Zanthoxylum bungeanum</i> Maxim. (<i>Z. bungeanum</i>) has attracted attention for its rich aroma. The aroma of <i>Z</i><i>. bungeanum</i> is mainly volatile terpenes synthesized by plant terpene metabolic pathways. However, there is little information on <i>Z. bungeanum</i> terpene metabolic gene. In this study, the coding sequence of <i>1-deoxy-D-xylulose-5-phosphate synthase</i> (<i>DXS</i>) and <i>farnesyl pyrophosphate synthase</i> (<i>FPS</i>) were cloned from <i>Z. bungeanum</i> cv. ‘Fengxiandahongpao.’ <i>ZbDXS</i> and <i>ZbFPS</i> genes from <i>Z. bungeanum</i> with CDS lengths of 2172 bp and 1029 bp, respectively. The bioinformatics results showed that <i>Z. bungeanum</i> was closely related to citrus, and it was deduced that <i>ZbFPS</i> were hydrophilic proteins without the transmembrane domain. Subcellular localization prediction indicated that <i>ZbDXS</i> was most likely to be located in chloroplasts, and <i>ZbFPS</i> was most likely to be in mitochondria. Meanwhile, the 3D protein structure showed that <i>ZbDXS</i> and <i>ZbFPS</i> were mainly composed of α-helices, which were folded into a single domain. In vitro enzyme activity experiments showed that purified proteins <i>ZbDXS</i> and <i>ZbFPS</i> had the functions of <i>DXS</i> enzyme and <i>FPS</i> enzyme. Transient expression of <i>ZbDXS</i> and <i>ZbFPS</i> in tobacco significantly increased tobacco’s terpene content. Moreover, <i>ZbDXS</i> and <i>ZbFPS</i> were expressed in different tissues of <i>Z. bungeanum</i>, and the relative expression of the two genes was the highest in fruits. Therefore, this suggests that <i>ZbDXS</i> and <i>ZbFPS</i> are positively related to terpene synthesis. This study could provide reference genes for improving <i>Z. bungeanum</i> breeding as well as for the Rutaceae research.