The taxonomy of Hydrochoerinae is confused because, until 2005, living capybaras and their extinct relatives were placed in their own family, Hydrochoeridae. Recent molecular phylogenetic studies recognize a close relationship between Hydrochoerus and Kerodon, supporting placement of both genera in a subfamily of Caviidae. Paleontological classifications have yet to incorporate this new taxonomy, and continue to use Hydrochoeridae for all capybaras, while using Hydrochoerinae for the living genus and its closest fossil relatives such as Neochoerus.
The classification of Hydrochoerinae is unclear because 2005 saw living capybaras and their extinct kin grouped separately in Hydrochoeridae. Recent molecular phylogenetic research indicates a close relationship between Hydrochoerus and Kerodon, suggesting they should be placed within the Caviidae subfamily. Paleontological classifications have not yet integrated this new taxonomy, still using Hydrochoeridae for all capybaras while employing Hydrochoerinae for the living genus and its closest fossil relatives such as Neochoerus.