Marine reef organisms often reside in highly fragmented patchworks of populations interconnected by dispersal of larvae through a hyper-variable ocean matrix. Understanding how and why such fragmented populations fluctuate is essential to predicting extinction risk and responses of populations to environmental change, management strategies, and harvest. Although larvae may routinely be “lost” from parental populations and “captured” by distant populations, we know virtually nothing about true movement potential of the young of most marine species. Using a novel application of moored and drifting light traps, we show that both assemblage-level comparisons and analyses of “environmental fingerprints” contained within the ear bones of larval fish can be used to characterize the effects of ocean matrix features on larval movements and hence connectivity among fragmented marine populations.