Stygofauna are any fauna that live in groundwater systems or aquifers, such as some caves, fissures and vugs. Stygofauna and troglofauna are the two types of subterranean fauna (based on life-history). Both are associated with subterranean environments – stygofauna are associated with water and troglofauna with caves and spaces above the water table. Stygofauna can live within freshwater aquifers and within the spaces of limestone, calcrete or laterite, whilst larger animals can be found in cave waters and wells. Stygofaunal animals, like troglofauna, are divided into three groups based on their life history - stygophiles, stygoxenes and stygobites.

1. Stygophiles inhabit both surface and subterranean aquatic environments, but are not necessarily restricted to either;
2. Stygoxenes are like stygophiles, except they are defined as accidental or occasional presence in subterranean waters. Stygophiles and stygoxenes may live for part of their lives in caves but do not complete their life cycle in them; and
3. Stygobites are obligate or strictly subterranean, aquatic animals and complete their entire life in this environment.