Integrating target capture with whole genome sequencing of recent and natural history collections to explain the phylogeography of wild‐growing and cultivated cannabis

Societal Impact Statement (EN) Cannabis has been used by humans for millennia, resulting in diverse landraces and uses. Its complex legal status and economic importance make sampling wild‐growing populations difficult, limiting past studies to modern cultivars with low genetic diversity. Our research provides crucial insights into the genetic diversity of wild‐growing and cultivated cannabis. We identified three major genetic groups—E Asia, Paleotropis, and Boreal—shedding light on evolutionary relationships within the genus. Understanding cannabis genetic structure supports conservation, sustainable breeding, and informed policy decisions. These findings lay a foundation for future research, ensuring the responsible use and preservation of this economically significant plant. Summary Cannabis has provided important and versatile services to humans for millennia. Domestication and subsequent dispersal have resulted in various landraces and cultivars. Unravelling the phylogeography of this genus poses considerable challenges because of its complex history. We relied on a Hyb‐Seq approach (combining target capture with shotgun sequencing), with the universal Angiosperms353 enrichment panel, to explore the genetic structure of wild‐growing cannabis accessions and cultivars by implementing phylogenomic and population genomic workflows on the same Hyb‐Seq data. Our findings support the treatment of Cannabis as a monotypic genus ( C. sativa L.), structured into three main genetic groups—E Asia, Paleotropis, and Boreal—with clear phylogeographic signal despite significant levels of admixture. The E Asia group was sister to the Paleotropis and the Boreal groups. Individuals within the Paleotropis group could be further structured into three subgroups: Iranian Plateau, C & S China and Himalayas, and Indoafrica. Individuals from the Boreal group split into two subgroups: Eurosiberia and W Mongolia and Caucasus and Mediterranean. Hemp and drug‐type landraces and cultivars consistently matched their putative geographic origin. These findings enhance our understanding of the genetic patterns in cannabis and provide a framework for future research into its current and past genetic diversity.