Developing survey strategies for threatened species is often limited by access to sufficient individuals to acquire information needed to design appropriate conservation measures. The goliath grouper (Epinephelus itajara) is a large reef fish, globally classified as critically endangered. In Brazil, fishing has been prohibited since 2002. Herein we investigated habitat use and abundance of E. itajara in Brazil drawn from a participative survey, which engaged volunteer divers in data-collection. A total of 188 reports were recorded between 2005 to 2011 throughout 13 Brazilian states. Our results revealed that habitat type influenced the relationship between total length and depth of occurrence of E. itajara. We observed a significant difference between habitats, artificial presented a nonlinear and natural an asymptotic relationship. This study underscores the importance of developing conservation measures addressing specific habitats and locations to enhance population recovery. Artificial structures (shipwrecks and manmade reefs) are critical habitats that must be considered as highly sensitive areas to E. itajara strategic conservation policies. We suggest the creation and implementation of marine protected areas, as key strategies for E. itajaraconservation, especially for artificial habitats and aggregation sites.