Coral reef ecosystems worldwide are facing increasing degradation due to disease, anthropogenic damage, and climate change, particularly in the Tropical Western Atlantic. Mesophotic coral ecosystems (MCEs) have been recently gaining attention through increased characterization as continuations of shallow reefs below traditional SCUBA depths (>30 m). As MCEs appear to be sheltered from many stressors affecting shallow reefs, MCEs may act as a coral refuge and provide larvae to nearby shallow reefs. The Deep Reef Refugia Hypothesis (DRRH) posits that shallow and mesophotic reefs may be genetically connected and that some coral species are equally compatible in both habitats. The research presented here addresses key questions that underlie this theory and advances our knowledge of coral connectivity and MCE ecology using the depth-generalist coral Montastraea cavernosa. Chapter 1 presents an overview of the DRRH, a description of MCEs in the Gulf of Mexico (GOM), and the framework of research questions within existing reef management infrastructure in the GOM. Through microsatellite genotyping, Chapter 2 identifies high connectivity among shallow and mesophotic reefs in the northwest GOM and evidence for relative isolation between depth zones in Belize and the southeast GOM. Historical migration and vertical connectivity models estimate Gulf-wide population panmixia. Chapter 3 focuses on population structure within the northwest GOM, identifying a lack of significant population structure. Dominant migration patterns estimate population panmixia, suggesting mesophotic populations currently considered for National Marine Sanctuary protection benefit the Flower Garden Banks. Chapter 4 quantifies the level of morphological variation between shallow and mesophotic M. cavernosa, revealing two distinct morphotypes possibly representing adaptive tradeoffs. Chapter 5 examines the transcriptomic mechanisms behind coral plasticity between depth zones, discovering a consistent response to mesophotic conditions across regions. Additionally, variable plasticity of mesophotic corals resulting from transplantation to shallow depths and potential differences in bleaching resilience between shallow and mesophotic corals are identified. The dissertation concludes with a synthesis of the results as they pertain to connectivity of shallow and mesophotic corals in the Gulf of Mexico and suggests future research that will aid in further understanding of MCE ecology and connectivity. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection