Fargesia is ecologically and economically important in mountainous forests. Many Fargesia species are also important sources of food for some endangered animals such as the giant panda. Recent molecular phylogenetic analyses have revealed Fargesia as a polyphyletic group despite some unclear lineage affinities. In the present study, we reconstructed the phylogeny of Fargesia and its allies, including Thamnocalamus, Arundinaria (incl. Bashania ), Yushania, Indocalamus, Ampelocalamus and Phyllostachys , from a plastome sequence matrix that contained 20 Fargesia and five Yushania species as ingroups, 16 species from nine other bamboo genera plus Oryza sativa and Zea mays as outgroups. Fargesia and its allies were broken into eight clades. Several Fargesia species were clustered into the Thamnocalamus clade and the Drepanostachyum + Himalayacalamus clade that rendered the polyphyly of Fargesia . The remaining six clades, including the Fargesia spathe clade, the Phyllostachys clade, Arundinaria fargesii , the Ampelocalamus clade, the Fargesia grossa clade, and the Fargesia macclureana clade, were identified. Molecular phylogenetic analyses supported that Yushania should be included in Fargesia (s.l.) which had synapomorphy of expanded leaf sheaths in varying degree at the basis of inflorescences, and further divided into the Fargesia spathe clade, the Fargesia grossa clade, and the Fargesia macclureana clade. All sampled species of Yushania were nested within the Fargesia grossa clade. The probable model of the origin of the species in the Fargesia spathe clade with spathe-like leaf sheath syndrome was proposed. Moreover, the formation of the spathe-like leaf sheath syndrome may be correlated with cold climatic conditions in Quaternary. Our results provide new sight into the phylogenetic relationship within Fargesia .

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The taxonomy of woody bamboo presents many difficulties due to its long blooming interval and complex morphological variation. Whether the current taxonomy reflects genuine species divergence within woody bamboo is an intriguing question. The Fargesia spathacea Franch. complex comprises 15 closely related species with a sympatric distribution in China. Their classification has long been controversial because only a handful of vegetative traits are available, providing a good opportunity to explore the evolutionary relationships and genetic differentiation in woody bamboo. Here, we present a study involving 750 individuals from 39 representative populations in the F. spathacea complex using 14 simple sequence repeat markers. We found varying degrees of genetic diversity across populations of the F. spathacea complex (He = 0.07–0.81) and largely negative F‐values at the population level, implying an excess of heterozygotes in the populations. Phylogenetic analyses revealed that all populations were divided into two major groups (clusters A and B), with the majority of the 15 species representing distinct genetic lineages. Based on population genetic analysis along with morphological evidence, we confirmed the identity of three species (F. decurvata J. L. Lu, F. spathacea, and F. murielae Gamble) and suggested the invalidation of four other species (F. scabrida T. P. Yi, F. robusta T. P. Yi, F. denudata T. P. Yi F. murielae (Gamble) T. P. Yi, and F. nitida (Mitford) Keng f. ex T. P. Yi). The delimitation of the remaining eight species has yet to be explored. The analysis of ecological factors and spatial autocorrelation suggested that altitudinal differences might account for the distinct genetic divergence between the two major groups.