We use mitochondrial DNA sequences to infer the origin and phylogenetic position of the Lesser Antillean species of the pitviper genus Bothrops, B. caribbaeus and B. lanceolatus. The two species form a monophyletic group, which in turn forms the sister clade to the Bothrops asper-atrox complex. High levels of sequence divergence among the Caribbean species, and between them and the nearest mainland relatives, suggest a relatively ancient origin of these snakes. The hypothesis that the Lesser Antillean Bothrops are the result of a recent colonisation event from within the South American B. atrox complex is rejected, as is the hypothesis that they were introduced to their island habitats by aboriginal humans. The high level of morphological apomorphy displayed by B. lanceolatus suggests a stepping-stone colonisation, St. Lucia being colonised first and then Martinique from St. Lucia. The medical implications of these findings are discussed: a recent case of envenoming from Saint Lucia suggests that Bothrops caribbaeus causes the same thrombotic syndrome of envenoming as B. lanceolatus.