Engineer species, such as gorgonians, provide several ecosystem services and play a significant role in the maintenance of biodiversity. We tested an ecological niche modelling an approach using a unique dataset of spatialized inventories on a regular grid (< 800 m) replicated in 2013 and 2020 along 450 km of coastline for five gorgonian species commonly found in the Mediterranean shallow habitats (10-50 m deep). Ten non-correlated environmental predictors derived from the most advanced geomorphological and hydrological data were used to assess the ecological niche of the five species using maximum entropy (Maxent). The model confirmed that different combinations of depth, rugosity, sea surface and bottom temperature, bottom flow speed and turbidity explain the different gorgonian’s distribution. The reduction of the number of presence observations did not alter the quality of the prediction as long as the observation points were spread over the entire variability range of predictors. The latter can be achieved by only including presence observations from highly protected zones of the marine protected areas of the region. Our results provide a greater understanding of the factors shaping the distribution of five gorgnian species commonly found in Mediterranean shallow areas.