This dissertation examines aspects of the relationship between connectivity and the development of genetic structure in subdivided coral reef populations using both simulation and algebraic methods. The first chapter develops an object-oriented, individual based method of simulating the dynamics of genes in subdivided populations. The model is then used to investigate how changes to different components of population structure (e.g., connectivity, birth rate, population size) influence genetic structure through the use of autocorrelation analysis. The autocorrelograms also demonstrate how relationships between populations change at different spatial and temporal scales. The second chapter uses discrete multivariate distributions to model the relationship between connectivity, selection and resource use in subdivided populations. The equations provide a stochastic basis for multiple-niche polymorphism through differential resource use, and the role of scale in changing selective weightings is also considered. The third chapter uses matrix equations to study the expected development of genetic structure among Caribbean coral reefs. The results show an expected break between eastern and western portions of the Caribbean, as well as additional nested structure within the Bahamas, the central Caribbean (Jamaica and the reefs of the Nicaraguan Rise) and the Mesoamerican Barrier Reef. The matrix equations provide an efficient means of modeling the development of genetic structure in subdivided populations through time. The fourth chapter uses matrix equations to examine the expected development of genetic structure among Southeast Asian coral reefs. Projecting genetic structure reveals an expected unidirectional connection from the South China Sea into the Coral Triangle region via the Sulu Sea. Larvae appear to be restricted from moving back into the South China Sea by a cyclonic gyre in the Sulu Sea. Additional structure is also evident, including distinct clusters within the Philippines, in the vicinity of the Makassar Strait, in the Flores Sea, and near Halmahera and the Banda Sea. The ability to evaluate the expected development of genetic structure over time in subdivided populations offers a number of potential benefits, including the ability to ascertain the expected direction of gene flow, to delineate natural regions of exchange through clustering, or to identify critical areas for conservation or for managing the spread of invasive material via elasticity analysis.