Recent studies have been collecting an increasing amount of evidence that the Hydropotinae is actually invalid. In several molecular studies, Hydropotes has allied closely with the roe deer (Capreolus: Capreolinae). Several morphological studies have also suggested that the water deer may in fact be an advanced deer that has secondarily evolved primitive characters.

Several features shared by roe deer and the water deer could be explained by a common evolutionary past. Both genera have a telemetacarpal foot structure (as do all members of the Capreolinae), are cold tolerant, and inhabit temperate regions rather than tropical ones (as one would expect from primitive cervids). While the ancestors of roe deer migrated into Asia from North America, the water deer has typically been seen as a historically Asian species. However, the distribution of Hydropotes in eastern Asia might be explained by a similar migration from the New World, the center of Capreolinae evolution.