Population assessments and species monitoring for many endangered marine megafauna are limited by the challenges of identifying and tracking individuals that live underwater in remote and sometimes inaccessible areas. Manatees can acquire scars from watercraft injury and other incidences that can be used to identify individuals. Here we describe a novel method for photo-identification of Antillean manatees Trichechus manatus manatus using aerial imagery captured during flights with a small multirotor drone. Between 2016 and 2017, we conducted 103 flights to detect and observe manatees in Belize, primarily at St. George's Caye (SGC) near the Belize Barrier Reef. Review of aerial videos from these flights resulted in 279 sightings of manatees (245 adults, 34 calves). High-resolution images of individual manatees were extracted and classified according to image quality and distinctiveness of individual manatees for photoidentification. High-quality images of manatees classified as sufficiently distinctive were used to create a catalog of 17 identifiable individuals. At SGC, 21% of all sighted adult manatees (N = 214) were considered photo-identifiable over time. We suggest that the method can be used for investigating individual site fidelity, habitat use, and behavior of manatee populations. Our photoidentification protocol has the potential to improve long-term monitoring of Antillean manatees in Belize and can be applied throughout clear, shallow waters in the Caribbean and elsewhere.