The Caribbean was one of the last regions of the Americas to be settled by humans, but how they reached the islands remains contentious. We analyzed genome-wide data for 93 individuals dating between 3200-400 cal. BP and find evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems to be connected to radiation events in North America. This was followed by a later expansion from South America, which is well attested archaeologically. We also detect clear genetic differences between the early settlers and the newcomers from South America with almost no evidence of admixture, raising questions regarding their interaction and the role of the early settlers in the development of later Caribbean societies.