Because whistles are most commonly associated with social delphinids, they have been largely overlooked, ignored, or presumed absent, in solitary freshwater dolphin species. Whistle production in the freshwater dolphin, the boto (Inia geoffrensis geoffrensis), has been controversial. Because of its sympatry with tucuxi dolphins (Sotalia fluviatilis), a whistling species, some presume tucuxi whistles might have been erroneously assigned to the boto. Using a broadband recording system, we recorded over 100 whistles from boto dolphins in the Yasunf River, Ecuador, where the tucuxi dolphins are absent. Our results therefore provide conclusive evidence for whistle production in Inia geoffrensis geoffrensis. Furthermore, boto whistles are significantly different from tucuxi whistles recorded in nearby rivers. The Ecuadorian boto whistle has a significantly greater frequency range (5.30-48.10 kHz) than previously reported in other populations (Peru and Colombia) that were recorded with more bandwidth limited equipment. In addition, the top frequency and the range are greater than in any other toothed whale species recorded to date. Whistle production was higher during resting activities, alone or in the presence of other animals. The confirmation of whistles in the boto has important implications for the evolution of whistles in Cetacea and their association with sociality.