Marine organisms with a pelagic stage are often assumed to display minor population structure given their extended larval development and subsequent high long-distance dispersal ability. Nonetheless, considerable population structure might still occur in species with high dispersal ability due to current oceanographic and/or historical processes. Specifically, for the wider Caribbean and Gulf of Mexico, theoretical and empirical considerations suggest that populations inhabiting each of the following areas should be genetically distinct: Panama, Belize, Southwest Florida (Tampa), and Southeast Florida (Fort Pierce). This study tests the hypothesis of significant genetic differentiation in Palaemon floridanus populations across the wider Caribbean and Gulf of Mexico. Population level comparisons were conducted using sequences of the mtDNA COI. In agreement with predictions, AMOVA and pairwise FST values demonstrated population differentiation among most pairs of the studied populations. Only Panama and East Florida populations were genetically similar. An isolation-with-migration population divergence model (implemented in IMA2) indicated that population divergence with incomplete lineage sorting can be invoked as the single mechanism explaining genetic dissimilarity between populations from the east and west coast of Florida. Historical demographic analyses indicated demographic expansion of P. floridanus in some localities [recent in Panama and ancient in East Florida and the wider Caribbean (entire dataset)] but constant population in other localities (in Belize and West Florida). This study rejects the idea of panmixia in marine species with high long-distance dispersal ability. Contemporary and historical processes might interact in a complex manner to determine current phylogeographic patterns.