Hybrid zones represent natural laboratories in which the processes of divergence and genetic isolation can be examined. The generation and maintenance of a hybrid zone requires mispairing and successful reproduction between organisms that differ in one or more heritable traits. Understanding the dynamics of hybridization between two species requires an understanding of the extent to which they have diverged genetically, the frequency of misparing and hybrid production, and the extent of introgression. Three hundred and twenty one blue-footed Sula nebouxii and Peruvian S. variegata boobies from the eastern tropical Pacific Ocean were analyzed using 19 putatively neutral genetic markers to evaluate interspecific differentiation, to classify morphological hybrids using Bayesian assignments, and to characterize hybridization using cline theory and Bayesian assignments. The species were well differentiated at mitochondrial and nuclear microsatellites, the hybrid zone was bimodal (contained a high frequency of each parental species but a low frequency of hybrids), and morphologically intermediate individuals were most likely F1 hybrids resulting from mating between female Peruvian boobies and male blue-footed boobies. Clines in allele frequency could be constrained to share a common geographic centre but could not be constrained to share a common width. Peruvian and blue-footed boobies hybridize infrequently, potentially due to strong premating reproductive isolation; however, backcrossing appears to facilitate introgression from blue-footed to Peruvian boobies in this hybrid system.