The Amazonian manateeTrichechus inunguishas been categorized as Vulnerable by the IUCN. There have been few studies on the species in its natural habitats due to its elusive nature and the low visibility of its aquatic habitats. Understanding the conservation status of Amazonian manatees, as well as any changes in their population trends and direct threats, is the basis for their management and conservation. Our study was carried out in 2 localities of the Ecuadorian Amazon (Tambococha-Jatuncocha and the Lagarto River), in the provinces of Sucumbíos and Orellana. We surveyed Amazonian manatees along rivers and in lagoons, using fish finder side-scan sonar to increase detectability rates. We estimated encounter rates, population density and occupancy. With a sampling effort of 573 km, we obtained an average encounter rate of 0.90 records 10 km-1and estimated a population density of 1.09 and 0.94 ind. km-2in Tambococha-Jatuncocha and the Lagarto River, respectively. In addition, occupancy rates varied between 0.51 and 0.57, and presence and distribution of the species were associated with distance to humans. The Amazonian manatee population estimates presented here represent a baseline for future research, and additional surveys will be needed to understand population fluctuations over time. An evaluation of population viability in Tambococha-Jatuncocha and the Lagarto River would also be required to determine whether these populations will be able to persist over the long term under different deterministic and stochastic scenarios.