The Viperidae is the most speciose family of Brazilian venomous snakes, with 33 known species. Although the family is well defined cladistically, there are few studies concerning the postcranial skeletal morphology, and only a single vertebral synapomorphy has been proposed. The paucity of knowledge on postcranial morphology poses challenges for the study of the Brazilian viper fossil record since most fossils consist of disarticulated and isolated vertebrae. Currently, Bothrops and Crotalus are the only vipers recognized in the Brazilian fossil record. Nonetheless, interspecific differentiation based on vertebral material is hampered due to the lack of comprehensive detailed anatomical data. We compared the trunk vertebrae of extant specimens of Crotalus and Bothrops using two-dimensional geometric morphometrics to obtain discriminant data about their vertebral morphology. We examined the trunk vertebrae of 20 vipers, 10 Crotalus, and 10 Bothrops and performed macroscopic analyses and measurements and landmark-based, two-dimensional geometric morphometric analyses. We sought to identify structural differences between the genera and to assess morphological variation along the spine. Most differences in the trunk vertebrae between Crotalus and Bothrops occurred in the length of the neural spine, the parapophyseal processes, the prezygapophyseal processes, and in the angle on the prezygapophyses. However, when we accounted for intracolumnar variation, differentiation is hampered. We expect our results will serve as a starting point for future studies of viperid vertebrae and aid paleontologists in accurately identifying fossil vipers.