The designation of subspecies has often been uncertain in systematics. In addition to phenotypic divergence, designation of subspecies may need to be supplemented by population genetic analyses. In this study, we perform such a survey of the mangrove tree Avicennia marina on Indo-West Pacific coasts. This species harbors three morphological groups. We collected samples from 16 populations (577 individuals) and sequenced 94 nuclear genes. Three genetic features support the subspecies designation for the three morphological subgroups. First, the observed genetic divergence is concordant with the morphological differences, with discordance found in zones of coexistence. Second, the three groups differ in the level of genetic diversity as well as in the demographic history, suggesting a degree of ecological differentiation. Third, and most important, the divergence level varies from locus to locus across the genome. A small portion of the genome is most informative about subspecies delineation, thus hinting the uneven exchange of genes. Such locus-dependent gene flow is expected for incompletely isolated groups. This last point suggests that the reduction in gene flow can be observed at some loci, thus hinting incipient reproductive isolation. In short, the three groups of A. marina appear to have evolved far beyond the stage of structured populations, but not to the point of full species. Hence, the subspecies designation is warranted. We believe these considerations can be generalized to other taxa.