Application of sidescan sonar at the regional scale of the Abrolhos Bank, with ground-truthing by remotely operated vehicles and mixed-gas diving operations, revealed a much more complex habitat mosaic than previously recognized. The regional benthic habitat map indicates 8844km2 of reefs (earlier estimates from remote sensing were around 500km2) and 20,904km² of rhodolith habitat—the world's largest continuous bed. Integration of the regional megahabitat map with spatially explicit data on the distribution of marine protected areas (<0.2% of each benthic megahabitat area) and economic activities with the highest potential of environmental impact (fishing, mining, oil and gas exploitation and dredging) reveals the need of a regional scale spatial planning process engaging conflicting sectors. •We present a benthic megahabitat map for the Abrolhos Shelf, with three megahabitats.•Benthic megahabitats include 8844km2 of reefs and the world's largest rhodolith bed with 20,904km².•Primary and secondary databases on the main economic activities and marine protected areas were integrated in the analyses.•Marine protected areas coverage is incipient and covers less than 0.5% of each megahabitat.•Elements for triggering spatial planning at the regional scale are presented and discussed.