The designation of subspecies has long been controversial in systematics. In addition to phenotypic divergence, subspecies designation may need to incorporate population genetic analyses. In this study, we perform such a survey on three subspecies of the mangrove tree Avicennia marina, distributed along the Indo-West Pacific coasts. Samples from 16 populations (577 individuals) were collected and 94 nuclear genes were sequenced. We identify four genetic features that support the subspecies designation in this genus. First, genetic divergence that delineates the three subspecies is evident, with discordance found mainly in zones of secondary contact. Moreover, levels of genetic diversity within local populations differ among subspecies. Second, the three subspecies have separate demographic histories inferred by computational modeling. Third, gene flow is detected between subspecies indicating little or no reproductive isolation. Fourth, the delineation of the subspecies varies from locus to locus across the genome, thus hinting continual but uneven exchanges of genes. All these features indicate that the three taxa have proceeded far beyond structured populations. Since they have not satisfied the criteria for full-species designation, the subspecies designation is warranted. We believe these considerations can be generalized to other taxa.