Studies of the feeding behaviour of aquatic species in their natural environment are difficult, since direct observations are rarely possible. In this study, a newly developed animal-borne underwater sound recorder (AUSOMS-mini) was applied to captive Amazonian (Trichechus inunguis) and Antillean (Trichechus manatus manatus) manatees in order to directly record their feeding sounds. Different species of aquatic plants were offered to the manatees separately. Feeding sounds were automatically extracted using a custom program developed with MATLAB. Compared to ground truth data, the program correctly detected 65–79% of the feeding events, with a 7.3% or lower false alarm rate, which suggests that this methodology is a useful recorder of manatee feeding events. All manatees foraged during both the daytime and night-time. However, manatees tended to be less active and masticated slower during the night than during the day. The manatee mastication cycle duration depended on plant species and individual. This animal-borne acoustic monitoring system could greatly increase our knowledge of manatee feeding ecology by providing the exact time, duration and number of feeding events, and potentially the plant species being fed on.