Chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important plant species growing worldwide. However, its origin, especially as revealed by biogeographic 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 spectrometry were used 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%. We studied different species from two hotspots which in similar geographical environments had closer chemotaxonomic relationships under the same cultivation conditions based on a cluster of 30 secondary metabolites. The average distribution altitude (ADA) differed significantly among Chrysanthemum, Ajania, and Phaeostigma in which it was 1227.49, 2400.12, and 3760.53 m.a.s.l. respectively, and the presence/absence of ray florets (RF) was significantly correlated with ADA (−0.62). 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 glacial–interglacial cycles, this region became their refuge, and they radiated and evolved from this center.

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