The temperate bamboos are a morphologically diverse grass lineage with a complex and problematic taxonomy. We present the first robust multilocus chloroplast phylogeny of the temperate bamboos, assess relationships among key genera with an emphasis on Arundinaria and its allies, and highlight the potential role of hybridization and reticulate evolution in this group. Utilizing a total of twelve plastid DNA regions (1 gene, 10 intergenic spacers, and 1 intron), the temperate clade was resolved to include six major lineages: Bergbamboes, the African alpine bamboos, Chimonocalamus, the Shibataea clade, the Phyllostachys clade, and the Arundinaria clade. Internal resolution varied among these six, in part reflecting sampling density and in part due to apparent evolutionary rate heterogeneity. The recovered phylogeny is largely incongruent with morphological classifications, rendering subtribes and many genera paraphyletic or polyphyletic. Some associations are consistent with existing hypotheses of intergeneric hybridization, while others may indicate convergent evolution, lineage sorting, or previously unsuspected cases of hybridization. Several robust lineages were identified within the Arundinaria clade, including the Medake subclade (Pleioblastus s. s. and allies), Sasa s. s., and the Sinicae subclade (comprising a subset of Chinese taxa currently classified in Acidosasa, Indosasa, Pleioblastus sect. Amari, and Pseudosasa subg. Sinicae). Our analyses also recovered a monophyletic Arundinaria s. s. in North America, and revealed substantial divergence between A. gigantea and A. tecta.
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