Recent advances in the development of individual-based bio-oceanographic larval dispersal models have opened up new opportunities for resolving complex connectivity patterns in marine environments. Combining the results of these types of models with matrix analysis, it is also possible to evaluate the expected development of genetic structure in large-scale population networks over time. Results for the Caribbean predict a strong east-west break, as well as a number of smaller, regional clusters (e.g. Mesoamerican Barrier Reef and Panama) and a cline through the Bahamas. In Southeast Asia, unidirectional gene flow appears to take place from the South China Sea into the Coral Triangle region via the Sulu Sea. Although the results are specific to the set of life-history characteristics adopted in the simulations, they are robust, and provide a means of bridging the gap between observed marine population genetic patterns and oceanographic processes.