Chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important plant species growing worldwide. However, its origin, especially in biogeography and metabolomics research, remains unclear. To understand the geographic distribution of species diversity and metabolomics in three genera (Chrysanthemum, Ajania and Phaeostigma), geographic information systems and gas chromatography-mass were involved in 19, 15 and 4 species respectively. China and Japan were two potential panbiogeographic nodes and diverse hotspots of Chrysanthemum with species richness ratios of 58.97% and 33.33%. Different species from two hotspots which in similar geographical environments had closer chemotaxonomic relationships under the same cultivation conditions based on 30 secondary metabolites cluster. The average distribution altitude (ADA) of Chrysanthemum, Ajania, and Phaeostigma increased significantly at 1227.49, 2400.12, and 3760.53Â m.a.s.l respectively, and ray florets (RF) was significantly correlated with ADA (â0.62). Mountain landform was an important contributor to global Chrysanthemum diversity, playing a key role in the divergence and distribution pattern of Chrysanthemum and its allies. The Hengduan Mountains-Qinling Mountains (HDQ) in China was a potential secondary radiation and evolution center of Chrysanthemum and its related genera in the world. During the Quaternary glacialâinterglacial cycles, the region became their refuge, radiated and evolved from this center.