<p>Assessing abundance and distribution of species is important for developing effective management strategies and facilitating monitoring. We investigated marine megafauna abundance and distribution at Aldabra Atoll, Seychelles with uncrewed aerial vehicles (UAVs). Forty-nine grid squares were flown in the west lagoon to estimate abundance, with one grid square repeated to look at tide effects. Generalized additive models were used to investigate whether habitat categories and environmental parameters correlate with the density and abundance of each taxon. We found that sea turtles, sharks and rays but not dugongs (likely due to small dugong sample size) show a significantly heterogeneous distribution. The overall observed density (individuals/km² ± SE) was 140.8 ± 18.7 for turtles, 19.0 ± 4.9 for sharks, 15.0 ± 2.2 for whiptail rays, 2.2 ± 0.7 for eagle rays, and 0.3 ± 0.1 for dugongs for the total surveyed area (17.1 km²). For all taxa, the presence or absence of land was a common best predictor for density. Time of day, presence of main benthic habitat type, and tide height were also included in best model predictors for various taxa. For tide surveys that were performed on one grid, tide height with date (one spring tide day and one neap tide day) as a random effect were in the top model results for all taxa (excluding dugongs). Hydrodynamics may influence distribution of megafauna in the surveyed grid, although there are likely other environmental factors that influence distribution which we may not have accounted for. This study provides essential insights for Aldabra’s management against the backdrop of global climate change and biodiversity loss, setting a conservation baseline, with specific hotspots for each group identified in the study area.</p>