Effective management of the threatened Antillean manatee (Trichechus manatus manatus) in Puerto Rico requires reliable estimates of population size. Estimates are needed to assess population responses to management actions, and whether recovery objectives have been met. Aerial surveys have been conducted since 1976, but none adjusted for imperfect detection. We summarize surveys since 1976, report on current distribution, and provide population estimates after accounting for apparent detection probability for surveys between June 2010 and March 2014. Estimates in areas of high concentration (hotspots) averaged 317 ± 101, three times higher than unadjusted counts (104 ± 0.56). Adjusted estimates in three areas outside hotspots also differed markedly from counts (75 ± 9.89 versus 19.5 ± 3.5). Average minimum island-wide estimate was 386 ± 89, similar to the maximum estimate of 360 suggested in 2005, but fewer than the 700 recently suggested by the Puerto Rico Manatee Conservation Center. Manatees were more widespread than previously understood. Improving estimates, locally or island-wide, will require stratifying the island differently and greater knowledge about factors affecting detection probability. Sharing our protocol with partners in nearby islands (e.g., Cuba, Jamaica, Hispaniola), whose populations share genetic make-up, would contribute to enhanced regional conservation through better population estimates and tracking range expansion.