A matrix-based projection model is used in conjunction with the results of a coupled bio-physical dispersal model to examine the spread of alleles through subdivided populations over time, and the associated development of genetic structural patterns. Applying this approach, it becomes possible to quantitatively evaluate the contribution of spatially explicit migration towards patterns of genetic structure observed in the field. To provide a concrete example, the model was used to examine genetic dispersal between coral reef patches of the Caribbean. Using generic life-history parameters, the model shows the formation of a strong genetic break between eastern and western patches, as well as the development of a gradient along the length of the Bahamian archipelago, corresponding with evidence previously collected for coral and fish species. The data also suggest that Jamaica and the Cayman Islands are important stepping stones between the reefs of the northern Caribbean (Hispaniola and the Bahamas) and the Mesoamerican Barrier Reef. The model provides an effective means of evaluating regional-scale genetic connectivity through time and identifying natural clusters of genetic exchange.