The temperate bamboos are a taxonomically difficult group with nearly 600 species in approximately 30 genera and at least 12 constituent lineages. In this study, phylogenetic relationships were explored using amplified fragment length polymorphism (AFLP) data in comparison with a phylogeny based on plastid DNA sequences, with an emphasis on Arundinaria of North America and its allies in East Asia (the Arundinaria clade). Molecular analyses involved 248 individuals in 10 genera and 60 species. Hybridization was detected both within and among genera. Comparative analyses indicated hybrid origins for species in several widespread and well-known genera, including Hibanobambusa, Sasaella, and Semiarundinaria. Evidence also indicated that Pseudosasa japonica (the type species of Pseudosasa) is an intergeneric hybrid involving Pleioblastus and Sasamorpha. In addition, cryptic hybrids were detected within and among Pleioblastus, Sasa, and Sasamorpha. After accounting for hybrids, phylogenetic analyses of AFLP data provided resolution for core lineages in the Arundinaria clade, including Pleioblastus sensu stricto, Sasa s. s., and Sasamorpha. AFLP data also provided evidence for the monophyly of the North American cane bamboos (Arundinaria, three species) but failed to identify their closest relative among the East Asian taxa. The broader evolutionary implications of hybridization in the temperate bamboos are discussed along with recommendations for future studies.