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The Alfred manta, Manta alfredi, is economically important in the Maldives due to the large number of tourists attracted to SCUBA dive and snorkel with them. It is important to understand the size of populations around main diving points and throughout the Maldives so that manta based tourism activities can be developed more successfully and the impact of tourism can be monitored. Using natural markings to identify individual manta rays, Petersen and Jolly-Seber probabilistic estimators were used to assess population size for main dive sites and the central atolls of North Male, Ari and Baa. Between 2000 and 2009, 1835 individual mantas were identified from 3373 sightings. There was a significant gender bias with a male: female ratio of 1:1.8. Only 24.7% of manta rays were re-sighted between 1 and 34 times with a maximum gap of 7 years and 11 months between sightings. Estimates for populations around main dive sites were 181–562. The estimated population of M. alfredi for North Male atoll is 537 (SE ± 53.2). Estimated atoll populations were extrapolated to obtain an estimate of Manta alfredi population for the entire Maldives of 9,677 individuals.