Reef fish in several islands of the Galapagos are affected via habitat deterioration, fisheries and water quality changes. Sound data acquisition and processing techniques to quantify the impact of anthropogenic pressures are therefore of paramount importance. In this study we developed an indicator system to assess the quality of fish communities. The evaluation is based on both taxonomic and trait-based approaches and allowed us to study ecosystem functioning and the role of certain species and groups in their habitats. The data were collected during a sampling campaign in 2017, during which reef fish were monitored via video recording of diver transects.