Seabirds are excellent ecosystem indicators and are amongst the most threatened taxa globally. Aldabra Atoll, Seychelles, supports significant breeding colonies of seabirds, especially red-footed boobies Sula sula. The population was surveyed by boat during 1968–1969 and in 2000, over which period the population grew from c. 6,500 to 10,000 breeding pairs. In 2022–2023, we monitored five subcolonies across Aldabra to determine breeding phenology and breeding success. In August 2022 and February 2023, we surveyed the atoll-wide population using the boat-based survey methodology followed in earlier studies. We also carried out unmanned aerial vehicle (UAV) surveys in February 2023 to compare the results with the boat-based counts and to quantify inland colonies undetectable by boat. Boat surveys revealed that Aldabra’s red-footed booby population had grown to 36,720 pairs by 2023, an increase that is intrinsically possible based on our population model but only if the much lower count in 2000 was an underestimate. The UAV and boat counts were closely aligned in our study, and aerial images captured a similar number of nests to boat surveys for shoreline colonies. However, UAV surveys revealed several undocumented inland colonies. An additional 5,574 inland breeding pairs of red-footed boobies were counted from images captured inland during aerial surveys in the 2023 wet season, bringing the atoll-wide population to at least 45,817 pairs. We recommend UAVs for surveys of large, conspicuous seabird species at low-lying mangrove colonies. Our study highlights the global importance of Aldabra as the most significant red-footed booby colony in the Indian Ocean and possibly the world.