The delimitation of evolutionarily significant units (ESUs) frequently results in controversy, but prioritising populations with evolutionary independence is essential for effective in situ conservation management. The American manatee (Trichechus manatus) is distributed along subtropical and tropical coastal waters from Florida (USA) to Alagoas (Brazil), and two subspecies are traditionally recognised, namely, T. m. latirostris, restricted to the Florida peninsula, and T. m. manatus, found in the remaining areas. However, this subspecific classification is not supported by genetic and morphologic evidence, which, rather, recognises two deeply differentiated populations or ESUs called Atlantic (Brazil) and Caribbean (from Venezuela to Florida). In this viewpoint paper, we compare both intraspecific divisions of T. manatus and the conservation implications. First, we used all available mtDNA evidence to test the genealogical clustering of the two American manatee ESUs by using a tree-based coalescent method. Second, we have used different models under a coalescent framework to estimate the historic gene flow among manatee populations. The analysis of the spatial distribution of mtDNA clusters confirmed the existence of the two suggested ESUs, rather than the two claimed subspecies. Furthermore, the best model to explain historic migration indicates that Brazilian manatees belong to an isolated population, whereas Florida and Caribbean populations are connected by more recent gene flow. These results have confirmed that T. manatus of the Caribbean, Gulf of Mexico and Florida belong to the same deme or Caribbean ESU, and the relatively isolated population inhabiting the Atlantic coast of Brazil belongs to the Atlantic ESU. Furthermore, both ESUs are separated by an interspecific hybrid zone (with the Amazonian manatee) located around the mouth of the Amazon River towards the Guianas coastline. The subdivision of two ESUs is also highly supported by karyotypic, morphological and ecological data, and is in clear disagreement with the traditional subspecies designations and the IUCN priorities, which manages Brazilian manatees as part of the Antillean manatee subspecies (T. m. manatus). Rather, Brazilian manatees should be considered as a full priority for conservation and require further taxonomic research; because of their deep history of isolation, they present high genetic and morphologic differentiation from all other American manatees.