Dataset associated with the paper "Analysis of Progress Towards a Comprehensive System of Marine Protected Areas in Brazil”. Data was collected using data compilation within Arc GIS 10.2. The habitat maps were derived from three sources: a subtidal benthic 20 map, built using high-resolution bathymetry data (Becker et al. 2009), and maps of 21 coral reef habitat (Brasil 2006) and mangrove ecosystems (Magris & Barreto 2011). 22 Depth zones, mangrove, coral reef habitat and ecoregions were used to define benthic 23 habitats. Study region spans all Brazilian coast. Data was collected to evaluate the performance of the Marine Protected Areas regarding conservation objectives for representation and persistence.