The Endangered Antillean manatee Trichechus manatus manatus is one of the most threatened aquatic mammal species in Mexico and the wider Caribbean region. The decline of this subspecies is mainly a result of historical exploitation and the impact of current coastal development. The conservation strategies adopted for the Antillean manatee include habitat protection, reduction of the most severe threats, and the rescue of stranded, orphaned or injured individuals and their management in captivity. This latter strategy has produced positive outcomes in some countries but has been the subject of controversy in others, including Mexico. We analyse the benefits and challenges associated with the management of captive manatees in Mexico, and the consequences of a lack of government policy and strategy for the post-rehabilitation release of individuals. We describe the evolution of this controversy from 1997–2017 in Mexico, analyse the consequences and implications for the conservation of the species, and propose an integrated management strategy that could address the issues raised. Although this strategy has been developed in the context of Mexico, it is applicable to management of this species across the Caribbean region.