Understanding the aggregation and habitat use patterns of a species can aid the formulation and improved design of management strategies aiming to conserve vulnerable populations. We used photo-identification techniques and a novel remote underwater camera system to examine the population sizes, patterns of residency and habitat use of oceanic (Mobula birostris) and reef (Mobula alfredi) manta rays in Seychelles (5.42°S; 53.30°E) between July 2006 and December 2018. Sightings of M. birostris were infrequent (n = 5), suggesting that if aggregation areas for this species exist, they occur outside of the boundary of our study. A total of 236 individual M. alfredi were identified across all surveys, 66.5% of which were sighted at D’Arros Island (Amirante Group) and 22.5% at St. François Atoll (Alphonse Group). Males and females were evenly represented within the identified population. M. alfredi visited a cleaning station at D’Arros Island less frequently during dawn and dusk than at midday, likely due to the adoption of a crepuscular foraging strategy. The remote and isolated nature of the Amirante and Alphonse Group aggregation areas, coupled with the lack of a targeted mobulid fishery in Seychelles, suggests that with appropriate regulations and monitoring, the marine protected areas gazetted within these two groups will benefit the conservation of M. alfredi in Seychelles.