ABSTRACTAmomi Fructus (Sharen, AF) is a traditional Chinese medicine (TCM) from three source species (or subspecies) includingWurfbainia villosavar.villosa(WVV),W. villosavar.xanthioides(WVX) orW. longiligularis(WL). Among them, WVV has been transplanted from its top-geoherb region Guangdong to its current main production area Yunnan for more than 50 years in China. However, the genetic and transcriptomic differentiation among multiple AF source (sub)species and between the origin and transplanted populations of WVV is unknown. In our study, the observed overall higher expression of terpenoid biosynthesis genes in WVV than that of WVX supplied possible evidence for the better pharmacological effect of WVV. We also screened ten candidateborneol dehydrogenase(BDH) genes that potentially catalyzed borneol into camphor in WVV. TheBDHgenes may experience independent evolution after acquiring the ancestral copies and the followed tandem duplications might account for the abundant camphor content in WVV. Furthermore, four populations of WVV, WVX and WL are genetically differentiated and the gene flow from WVX to WVV in Yunnan contributed to the increased genetic diversity in the introduced population (WVV-JH) compared to its top-geoherb region (WVV-YC), which showed the lowest genetic diversity and might undergo genetic degradation. In addition,TPSandBDHgenes were selected among populations of multiple AF source (sub)species and between the top-geoherb and non-top-geoherb regions, which might explain the metabolite difference of these populations. Our findings provide important guidance for the conservation, genetic improvement, industrial development of the three source (sub)species, and identifying top-geoherbalism with molecular markers and proper clinical application of AF.