Species in the genus Bothrops s. l. are extraordinarily variable in ecology and geography, compared with other genera in the subfamily Crotalinae. In contrast to the trend of splitting large and variable groups into smaller, more ecologically and phenotypically cohesive genera, the genus Bothrops has remained speciose. In addition, previous phylogenetic analyses have found Bothrops to be paraphyletic with respect to the genus Bothriopsis. Taxonomic arguments exist for synonymizing Bothriopsis with Bothrops, and for splitting Bothrops into smaller genera, but the greatest hindrance to taxonomic revision has been incomplete phylogenetic information. We present a phylogeny of Bothrops, Bothriopsis, and Bothrocophias based on 85 characters of morphology and 2343 bp of four mitochondrial gene regions, and with significantly greater taxonomic coverage than previous studies. The combined data provide improved support over independent datasets, and support the existence of discrete species groups within Bothrops. The monophyly and distinctness of these groups warrant recognition at the generic level, and we propose a new taxonomic arrangement to reflect these findings. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156, 617–640.