* Premise of the study: Hybridization is common in both animals and plants and can lead to a diverse array of outcomes ranging from the generation of new ecotypes or species to the breakdown of morphological differences. Here, we explore the extent of hybridization in the three currently recognized New World Rhizophora species--R. mangle, R. racemosa, and the putative hybrid species R. harrisonii. * Methods: We assayed variation across the three recognized Rhizophora species using two noncoding chloroplast (cpDNA), two flanking microsatellite regions (FMRs), and six microsatellite loci. * Key results: Gene genealogies of cpDNA and FMRs showed a strong phylogeographic break across the Central American Isthmus, but little relationship to recognized species boundaries. Instead, individuals collected in the same ocean basin and classified as R. mangle and R. racemosa by morphological characteristics were more closely related to each other than with similar looking individuals collected in the other ocean basin. Nonetheless, there were low, yet significant differences at microsatellite loci among co-occurring populations of R. mangle and R. racemosa in both ocean basins, suggesting that two taxonomic groups coexist. However, we found no genetic evidence that R. harrisonii was a hybrid species. Rather, R. harrisonii appears to represent a morphotype produced by ongoing hybridization and backcrossing between R. mangle and R. racemosa. * Conclusions: Our data support ancient and persistent introgressive hybridization among new world Rhizophora and argue for a full revision of the systematic relationships of the group based on much finer morphological, ecological, and genetic analyses.
