The Florida Keys National Marine Sanctuary (FKNMS) encompasses North America's only living coral barrier reef and the third longest barrier reef in the world, making it a unique national treasure of international notoriety (FKNMS, 2005). Recent evidence of environmental decline within the sanctuary has created a sense of urgency to understand and protect the valuable resources within. This thesis contributed to the understanding of habitat connectivity to aid managers and decision makers in the creation of additional Marine Protected Areas (MPAs) in the FKNMS to help prevent further environmental decline. This research specifically focused on modeling larval transport and larval connectivity among Acropora palmata (Lamarck, 1816) populations, coral habitats and MPAs in the upper and middle FKNMS. The transport of larvae in relation to ocean currents is a very limited area of research, and the analytic modeling results may serve as powerful guides to decisions about the relative importance of individual coral habitats and MPAs in the study area.Larval transport was modeled with ArcGIS and TauDEM using SoFLA-HYCOM simulated ocean currents during the A. palmata spawning season. This model allowed for the assessment of coral habitat and A. palmata population larval connectivity. The dependence of three distant A. palmata test populations on other upstream coral habitats and A. palmata populations significantly differed (Kruskal-Wallis test, P less than 0.0001). The clonally diverse Sand Island Reef A. palmata population's larval connectivity was significantly higher compared to other distant monoclonal populations (Mann-Whitney test, P less than 0.0001). Compared to the clonal structure of each test population determined by Baums, Miller, and Hellberg (2006), results indicated simulated larval connectivity may be a determinant of A. palmata population clonal diversity.By modeling MPA and coral habitat connectivity, this study also identified unprotected and distant coral habitat areas with the greatest downstream influence on MPAs; these may serve as potential coral larvae sources. It is recommended that establishing these areas as no-take MPAs would improve overall coral habitat and MPA network connectivity.