Site-specific knowledge of spatial ecology is essential for the implementation of effective conservation measures for wide-ranging marine species. We used passive acoustic telemetry to examine the movements and site usage of reef manta rays Mobula alfredi in the Inhambane Province of Mozambique. Acoustic receivers were installed at 14 sites spanning 350 km along the coastline. We deployed 42 acoustic transmitters on manta rays between February 2010 and November 2014. Using Brownian bridge kernel utilization distributions, (bbKUD), we estimated core (50 % bbKUD) and extent (95 % bbKUD) home ranges, and constructed spatial movement networks to examine connectivity. Manta rays exhibited site affinity and diel visitation patterns to cleaning stations, with 89.2% of detections during daylight hours, and spent up to 8.2 h at these sites (mean visit duration = 25.41 ± 2.45 min). Manta rays moved widely within the study region, and strong connectivity was evident between Praia do Tofo and Zàvora. However, no movements were recorded between the Bazaruto Archipelago and the southern sites. Existing marine protected areas (MPAs) offer protection across ~24% of the estimated extent home range, and only to animals that use the waters of the archipelago. We therefore suggest the explicit protection of critical habitats through spatial management approaches in Praia do Tofo and Zàvora and the expansion of current MPA boundaries in the Bazaruto Archipelago. Ideally, these measures should be re-enforced by prohibiting directed fishing of manta rays in Mozambique and additional restrictions on gill net usage to prevent incidental capture outside of protected areas.