Pterocarpus officinalis is a significant component of the Caribbean wetland plant community. Currently, stands are growing near their physiological extreme, thus it is very important to understand the biology of the species to develop effective conservation strategies and plans. The intra-specific diversity of P. officinalis has been analyzed at different spatial scales, from the continental to the insular Caribbean areas, by using AFLP, chloroplast and nuclear microsatellites, cpDNA, and nrITS markers. The genetic diversity of P. officinalis was higher from continental than from island populations. A similar pattern of genetic diversity resulted from Bradyrhizobial strains isolated from P. officinalis nodules. Bradyrhizobial strains associated with P. officinalis have positive effects on nodulation, N-acquisition, and plant growth. Pterocarpus officinalis is not a halophyte plant. However, it grew better in flooding due to the lenticels, adventitious roots, and aerenchyma that promote root colonization by arbuscular mycorrhizal fungi (AMF) and N-fixing root-nodular bacteria. Furthermore, arbuscular mycorrhizal colonization and nodulation improve flooding tolerance in P. officinalis seedlings. The ecological, demographic, genetic, and physiological data that have been collected through the Caribbean populations of P. officinalis in combination with data from its associated microorganisms are providing the framework to develop better restoration efforts for the species.