The absence of terrestrial apex predators on oceanic islands led to the evolution of endemic secondary apex predators like birds, snakes and crocodiles, and loss of defence mechanisms among species. These patterns are well documented in modern and Quaternary terrestrial communities of the West Indies, suggesting that biodiversity there assembled similarly through overwater dispersal. Here, we describe fossils of a terrestrial apex predator, a sebecid crocodyliform with South American origins from the late Neogene of Hispaniola that challenge this scenario. These fossils, along with other putative sebecid specimens from Cuba and Puerto Rico, show that deep-time Caribbean ecosystems more closely resembled coeval localities in South America than those of today. We argue that Plio-Pleistocene extinction of apex predators in the West Indies resulted in mesopredator release and other evolutionary patterns traditionally observed on oceanic islands. Adaptations to a terrestrial lifestyle documented for sebecids and the chronology of West Indian fossils strongly suggest that they reached the islands in the Eocene–Oligocene through transient land connections with South America or island hopping. Furthermore, sebecids persisted in the West Indies for at least five million years after their extinction in South America, preserving the last populations of notosuchians yet recovered from the fossil record.