The critically endangered coral species Acropora palmata used to dominate shallow Caribbean reefs but since the early 1980s, populations have dramatically declined. At the Caribbean scale, A. palmata is divided into two genetically divergent lineages and most of previous works investigating population connectivity among populations involved the western lineage (in Florida, the Bahamas, the Mesoamerican Reef System, and the Greater Antilles). Small scale genetic connectivity among A. palmata populations was globally found, possibly enhancing populations’ recovery at the local scale. Yet, little is known regarding the genetic connectivity of populations of the eastern lineage, especially those of the Lesser Antilles, a fragmented archipelago located at the edge of the species distribution. Here, we filled this gap by investigating the genetic diversity, population structure and connectivity of A. palmata populations among 36 sampled sites from 11 islands of the Lesser Antilles using 14 hypervariable microsatellite loci. Globally, genetic diversity levels in A. palmata populations from the Lesser Antilles were lower compared to what was previously reported within the Wider Caribbean. The analysis of the genetic structure, crossed with spatial autocorrelation analysis, revealed an isolation-by-distance pattern at both reef and Lesser Antilles scales. A gene dispersal distance of less than a kilometer, and a northward gene flow direction, in agreement with ocean surface currents in the region were found. Altogether, our results suggest a restricted population connectivity and short distance dispersal of A. palmata larvae within the Lesser Antilles further limited by geographic distances among suitable habitat patches. Additionally, our results suggest that southernmost populations are potential sources of larvae for the most northerly islands and have a key role in reseeding A. palmata populations of the Lesser Antilles.