This dissertation describes the reproductive biology and patterns of genetic diversity of the endangered tropical tree Guaiacum sanctum (Zygophyllaceae). First, I analyzed the abundance and spatial distribution of different size classes of G. sanctum within Palo Verde National Park (PVNP). Results showed a large proportion of individuals in the smaller size categories, suggesting population growth. All size classes were spatially aggregated and associated with canopy openings; seedlings occurred in shaded areas and saplings and juveniles were found in open areas. Allozyme analyses were used to examine patterns of fine-scale genetic structure (FSGS) in three plots within PVNP. A lack of fine-scale genetic structure was observed for all size classes, suggesting the mixing of seeds from several different adults. A parent-pair analysis indicated that populations of G. sanctum populations were probably established by bird mediated long-distance seed dispersal.To broaden the spatial scale, I quantified genetic diversity within and among seven G. sanctum populations in Costa Rica. I compared genetic diversity differs between populations in continuous habitats and trees in fragmented sites. Results indicated that G. sanctum maintains high levels of genetic diversity. Trees in fragmented habitats did not have less genetic diversity than trees in protected habitats. We concluded that the observed patterns of genetic structure in this species are probably caused by the historic separation of populations in different geographic regions, and extensive historical rates of gene flow among populations within regions. To determine if fragmentation has affected gene-movement, I estimated the mating system and pollen flow patterns of G. sanctum. A fractional paternity analysis was used to estimate average gene flow distances. Our results showed that G. sanctum is a mixed-mating species with the ability to transport pollen over large distances. Isolated trees function as stepping-stones between clusters of individuals, assisting long-distance pollen movement. These individuals also sired a disproportionate number of seeds, and are thus important components of the reproductive success of the population. The high levels of genetic diversity maintained as a consequence of long-distance gene-flow suggest that this endangered species may have the potential for future adaptation and population expansion.