Assessments of individual animal health alerts to early signs of population level effects in wildlife but often rely on logistically complex wild animal captures, hindering our understanding of the wellbeing of populations in regions with limited resources. Here, we tested photogrammetry methods using small aerial drones for accurate morphometric measurements of Antillean manatee (Trichechus manatus manatus) body size and body condition. We flew drones to collect aerial imagery of captive manatees in Quintana Roo, Mexico and compared manatee body size measurements from scaled aerial imagery with physically measured body sizes. To assess optimal altitude for imaging, body size measurements acquired with an out-of-the-box drone were compared to measurements from the same drone model equipped with a LiDAR for precision altimetry flown at three altitudes (30 m, 50 m, 70 m). The accuracy of body size measures was similar for all drone models but improved with the addition of LiDAR. Difference in body size estimates between manual and drone-based measurements indicate a correction factor may be needed to account for disparities. We then used body size measurements to develop a body condition index for Antillean manatees. Our findings highlight the strength of low-cost aerial drones for morphometric measurements and assessments of manatee body condition.