Abstract: Encephalartos, an African endemic genus within the Zamiaceae, comprises 65 extant species whose phylogenetic relationships have remained unresolved due to limited genetic differentiation observed in previous studies. This research reconstructs the evolutionary history of Encephalartos utilizing 3545 single‐copy nuclear genes derived from transcriptomes of 64 species. The study estimates divergence times and reconstructs ancestral states for 12 key morphological traits. Phylogenetic analyses definitively resolve eight major clades, supported by both molecular and morphological evidence. Although these clades partially align with previous morphology and geography based classifications, the genomic data provide novel insights, necessitating a revised infrageneric system. Biogeographic reconstructions indicate that Encephalartos originated in southern Africa during the Oligocene (~26.3 Ma), subsequently dispersing into eastern and northern Africa through the Zimbabwe–Mozambique corridor during the Miocene, followed by expansion into Central Africa. Speciation rates decreased markedly during the Pliocene and Pleistocene, potentially due to intensified climatic drying and cooling. Morphological character mapping identified ancestral traits, including aerial stems, green leaves, and red sarcotesta. Specific transitions such as subterranean stems in clade IV and bluish‐green leaves in clades II and V, further substantiate clade differentiation. These findings resolve long‐standing taxonomic uncertainties and emphasize the Oligocene‐Miocene as a crucial period for Encephalartos diversification, influenced by Cenozoic climate change. This research establishes a robust framework for future systematic and conservation studies while demonstrating the effectiveness of transcriptome data in resolving phylogenies of slowly evolving lineages.

Key words: biogeography, cycads, Encephalartos, phylogenetics, transcriptome data, Zamiaceae