<p>Assessing population responses to anthropogenic impacts is crucial for effective conservation management. However, estimating the abundance and demographic parameters of vulnerable marine megafauna presents significant logistical and financial challenges, particularly in developing nations with limited resources and infrastructure. This study provides the first comprehensive population abundance analysis for reef manta rays (<i>Mobula alfredi</i>) in Nusa Penida, Bali, Indonesia, a region adjacent to former targeted manta ray fishing grounds. Additionally, it is only the second such analysis for this species in Indonesia. We used POPAN Jolly–Seber and Robust Design capture-mark-recapture models from an 11-year photo-identification dataset (2012–2023) collected by researchers and citizen scientists. Annual abundance estimates ranged from 170 (95% CI = 154–198.6) in 2012 to 447 (95% CI = 393.6–517.6) in 2022, indicating an overall increase in abundance during the study period, with high rates of apparent survival (mean = 0.92, SE = 0.02, 95% CI = 0.88–0.94). The proportion of individual manta rays sighted more than once (79.5%) was higher than in any other documented manta ray aggregation elsewhere in the Indo-Pacific region. Our results also suggest that citizen science contributions improved the accuracy of abundance estimates. Continued long-term monitoring of individual manta rays at this aggregation, both through dedicated research and the involvement of citizen scientists, is required to monitor population status and detect changes in relation to anthropogenic impacts, particularly fisheries bycatch, climate change, and tourism.</p>