水豚亚科（Hydrochoerinae）是豚鼠科下的一个亚科，其下所有属中只有两个还有存活物种，即水豚属和岩豚鼠属。不过在2005年之前，水豚和其亲缘种还都分在水豚科下（Hydrochoeridae）， 后来基于生物系统发生学证据将其划入亚科。 但是一些古生物分类还依然采用旧的方法。 其远古近亲的分类地位中所包含的生物数量已经大大减少。 主要是水豚及其亲缘动物的臼齿在不同种之间差异太大。 例如曾经根据不同的臼齿划出过四属七种不同生物，但现在被认为它们只是不同年龄段的Cardiatherium paranense而已。

The Hydrochoerinae are a subfamily of Caviidae, consisting of two living genera, Hydrochoerus, the capybaras, and Kerodon, the rock cavies. In addition, a number of extinct genera related to capybaras should also be placed in this subfamily. 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 taxonomy of fossil hydrochoerines is also in a state of flux. In recent years, the diversity of fossil hydrochoerines has been substantially reduced. This is largely due to the recognition that capybara molar teeth show strong variation in shape over the life of an individual. In one instance, material once referred to four genera and seven species on the basis of differences in molar shape is now thought to represent differently aged individuals of a single species, Cardiatherium paranense.