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The Central American Isthmus (CAI) is an important geographic barrier in the Neotropics. Its role in the diversification of marine and coastal species has been detected in fishes, turtles, sea urchins, and mangroves. We evaluated the CAI’s influence on the diversification of the most ancient neotropical mangrove species Pelliciera rhizophorae across populations from the Caribbean and Pacific coasts, based on the analysis of ten nuclear microsatellite loci and two noncoding chloroplast DNA regions. The two molecular markers showed concordant patterns of diversification in this mangrove species. Contrary to our expectations, this study did not reveal significant genetic structure among populations separated by the CAI. Two major genetic variants (cluster I and cluster II) were found on both coasts, but the two were not found intermixed in the same population. Within each coastal region, breaking of gene flow …