Enthusiasm for the use of no-take marine protected areas (MPAs) as management tools for the protection and enhancement of coral reef fishes is widespread. However, evidence that such marine reserves actually enhance fishery yields is limited, primarily because of difficulties in quantifying the exchange of individuals—especially larvae—between local populations within and outside the protected area. Knowledge of the extent and spatial scale of this connectivity is of vital importance for the effective design and implementation of marine reserves intended as fishery management tools. We review our current understanding of connectivity among coral reef populations, including the role of important determining factors such as pelagic larval duration, larval behavior, and hydrodynamics. We also discuss artificial and natural tagging methods that potentially can be used to track movements of larvae between marine reserves and surrounding waters. To illustrate the application of such methods, we discuss ECONAR (Ecological CONnections Among Reefs), a new, regional-scale research project designed to measure the extent of connectivity among populations of coral reef fishes in the Mesoamerican Barrier Reef System.