Reef manta rays Mobula alfredi are large filter-feeding elasmobranchs that are undergoing substantial population declines on a global scale. In order to effectively conserve and manage populations, it is crucial that the drivers of their occurrence are defined and that key aggregation areas for this species are identified and protected. Here, we used passive acoustic telemetry to monitor and assess the movement ecology of M. alfredi in the remote Amirante Islands, Republic of Seychelles. Acoustic transmitters were externally deployed on M. alfredi at D'Arros Island (n = 42) and movement data retrieved from an array of 70 acoustic receivers deployed throughout the Amirantes between November 2013 and October 2017. Individuals were detected year-round, with a peak in detections occurring between November and April coinciding with the arrival and departure of the north-west monsoon. Individuals were most likely to be detected within the array during the day, at low wind speeds, and when water temperatures were approximately 28°C. Additionally, individuals were more likely to be detected during a new moon, when the tidal range was at its highest, and on the slack of high tide. M. alfredi travelled widely within the Amirantes, with larger individuals travelling greater distances per day than smaller individuals and juveniles. The majority of detections (89%) were recorded within 2.5 km of the shoreline of D'Arros Island and the neighbouring St. Joseph Atoll, highlighting the importance of these sites to M. alfredi in the Amirante Islands, and supporting the proposed development of a marine protected area at this location.