This study explores the application of small, commercially available drones to determine morphometric the measurements and record key demographic parameters of reef manta rays (Mobula alfredi) in Raja Ampat, Indonesia. DJI Mavic 2 Pro drones were used to obtain videos of surface-feeding M. alfredi with a floating, known-length PVC pipe as a reference scale—thus avoiding the need to utilize altitude readings, which are known to be unreliable in small drones, in our photogrammetry approach. Three dimensions (disc length (DL), disc width (DW), and cranial width (CW)) from 86 different individuals were measured. A hierarchical multivariate model was used to estimate the true measurements of these three dimensions and their population-level multivariate distributions. The estimated true measurements of these dimensions were highly accurate and precise, with the measurement of CW more accurate than that of DL and, especially, of DW.