Phylogenetic studies of present-day terrestrial organisms indicate that faunal dispersals between South America and the Greater Antilles have occurred during the Cenozoic. However, due to the absence of regional paleogeographic reconstructions based on geological data, the migration paths of their ancestors along the eastern boundary of the Caribbean plate, i.e. the Lesser Antilles trench, remains unknown. We present novel paleogeographic maps of the central Lesser Antilles (extending from Guadeloupe to Martinique islands). Based on onshore and offshore stratigraphic correlations (50 seismic lines, biostratigraphy of 9 dredged and 29 field samples, six sedimentary logs), we unravel repetitive episodes of uplift and drowning that have occurred in the central part of the Lesser Antilles during the Neogene. Offshore, the Marie-Galante Basin comprises three sedimentary megasequences that deposited between: (i) the Oligocene and Early Miocene, including the ancient arc, (ii) the Middle and Late Miocene and (iii) the Latest Miocene and Holocene. These sediments infill a NNW-SEE trending forearc rift that opened during Early Miocene. The megasequences are separated by subaerial regional unconformities that affect the rift shoulders. Onshore, we show that the lower part of the carbonate platform in Guadeloupe and La Désirade deposited during the Late Messinian. In Martinique, we refine the age of the carbonate deposits belonging to the extinct arc to the Chattian-Burdigalian, and evidence a major subaerial unconformity corresponding to the Middle Miocene. Finally, based on our results and available data, we propose a reconstruction of the paleogeographic evolution of the Lesser Antilles through the Neogene from Anguilla to the north to Martinique to the south. Our work evidence that large, now sunken archipelagos have existed there during the early Middle Miocene and the latest Miocene. We suggest that during the Miocene, the Lesser Antilles may have been used as a pathway for land-faunal dispersals from South America.