The biological diversity is a natural inherent element of social-ecological systems. Within the great species diversity there is a group of small invertebrates (2–20 mm), inhabiting terrestrial soils and aquatic sediments, known as macrofauna. Contrary to its name indicates, the macrofauna is generally overlooked, poorly represented in biological inventories or management programs, and not contemplated in any political agenda, but they consist of high number and many groups of species with a high diversity in shapes and functions. Knowing this diversity and their functions in both terrestrial and aquatic habitats is fundamental to understand its role within the social-ecological systems, by giving key information that would advance our comprehension on the role of macrofauna in the quality of environmental services provided by ecosystems. Furthermore, this understanding is crucial due to the fact that the macrofauna is threatened by anthropogenic activities, which could lead to local modifications in the processes that take place in the soil. Therefore, the purpose of this work is, in general, to make known to the reader the main species groups that integrate the macrofauna, the equivalent functional role that these organisms play in the terrestrial and aquatic habitats where they occur, as well as their importance in studies of sustainability in tropical social-ecological systems. Keywords: Biodiversity, benthic macrofauna, edaphic macrofauna, functional traits, ecosystems.