The reef manta ray Mobula alfredi is present throughout most island groups that form the Raja Ampat archipelago, Indonesia. The species is protected regionally and nationally and is currently managed as a single homogeneous population within the 6.7 million ha archipelago. However, scientific evidence is currently lacking regarding the spatial connectivity and population structure of M. alfredi within this archipelago. Using network analysis and an array of 34 acoustic receivers deployed throughout Raja Ampat between February 2016 and September 2021, we examined the movements of 72 subadult and adult M. alfredi tagged in seven regions of Raja Ampat. A total of 1094 M. alfredi movements were recorded and were primarily concentrated between nearby receiver stations, highlighting frequent local movements within, and limited long-distance movements between regional acoustic receiver arrays. Network analysis revealed highly connected nodes acting as hubs important for M. alfredi movements. A community detection algorithm further indicated clusters within the network. Our results suggest the existence of a metapopulation comprising three demographically and geographically distinct subpopulations within the archipelago. They also reveal the importance of Eagle Rock as a critical node in the M. alfredi movement network, justifying the urgent inclusion of this site within the Raja Ampat marine protected area network.

Indonesia is home to significant populations of globally vulnerable reef manta rays (Mobula alfredi) in at least four key regions: Berau, Nusa Penida, Komodo, and Raja Ampat. Despite detailed population studies in each of these regions, little is known about their horizontal movement patterns. Our study used satellite telemetry to investigate reef manta rays’ habitat use and home ranges. A total of 33 manta rays were tagged with SPLASH10F-321A satellite tags across the four regions: Berau (n = 5), Nusa Penida (n = 8), Komodo (n = 6), and Raja Ampat (n = 14), yielding usable data from 25 tags. The rays were tracked for 7 to 118 days (mean ± SD = 50 ± 30) from July 2014 to July 2022. The results showed localized movements, strong residency near tagging sites, and high site fidelity as evidenced by area-restricted search (ARS) behaviors and frequent revisitations. Most manta rays showed restricted home ranges in each region, with no connectivity between regions. Across 25 individuals, the home range (95% utilization distributions) varied significantly, ranging from 19 to 48,294 km² (mean ± SD = 4667 ± 10,354). These findings offer important insights into the spatial movement patterns of reef manta rays in Indonesia, allowing the formulation of more effective management strategies.