This dissertation describes the genetic population status of the threatened Caribbean hard coral, Acropora palmata. Specifically, I determined the genotypic diversity within local populations of this coral, and the extent to which geographically isolated populations were genetically similar, information that is essential for future conservation and recovery efforts. To achieve this I developed highly polymorphic genetic markers (microsatellites) and tested their inheritance patterns via controlled crosses. Application of these markers to 1051 colonies sampled throughout the Caribbean identified an eastern and a western phylogeographic province for Acropora palmata, with little or no recent gene exchange between them. The split most likely occurs along a north-south running line between the Mona Passage to the Peninsula de Guajira, Colombia. Larval dispersal within each province is asymmetrical, with some reefs serving as larval sources while others are sinks. Larval sources are largely self-recruiting. The discovery of subdivision in an organism with a long planktonic larval stage within an area marked by strong current flow challenges the notion of open local populations in Caribbean broadcast spawning corals. Across the sampled region, sexual reproduction contributed to about 50% of the population structure. Within provinces, sexual reproduction was more important in the east than the west. The Florida Keys, part of the western province, were showed the highest degree of clonal replication, following predictions on the rising importance of asexual reproduction in marginal habitats. Both within the western and the eastern province, denser stands were dominated by asexual reproduction while less dense stands were more sexual. Clonal structure was unpredictable on smaller spatial scales. This study provided data addressing the current debate about open or closed marine populations. New molecular tools and statistical methods as well as a broad geographical sampling design were essential in describing both gene flow patterns and local modes of reproduction.