We explored the patterns of intra‐ and interpopulation variation in flower morphology of the red mangrove, Rhizophora mangle. Twelve populations in Mexico were studied: five from the Gulf of Mexico and the Caribbean Sea, and seven from the Pacific Coast. Six metric floral attributes were measured from a sample of 1370 flowers. Significant differences among populations were found for all six attributes. Because floral attributes were all correlated, scores derived from principal factor analysis were used to describe the variation in flower morphology. Two factors explained essentially all of the variance in flower morphology. Corolla and calyx size had a strong effect on factor 1, while gynoecium size had the higher effect on factor 2. Nested analyses of variance on the scores from both factors revealed significant differences among coasts, among populations within coasts, and among plants within populations. Nonetheless, this variation cannot be explained as a result of clinal variation, as indicated by a series of regression analyses. Cluster analysis (UPGMA) showed that a population from the Pacific coast was clustered together with those of the Atlantic, and the arrangement of populations within each coast showed no evident geographical pattern. We propose that frequent events of extinction and recolonization by a few individuals, followed by selfing, may produce differentiation among populations of red mangrove.