Hybridization can either reinforce or erode species boundaries; therefore, hybrid zones offer a natural experimental setting in which to assess the dynamics of reproductive isolation. Secondary contact zones, in particular, present a partial separation of the original divergence mechanisms and the subsequent genomic architecture of reproductive isolation (or lack thereof). The spatial context of secondary contact and its consequent effect on dispersal play vital roles on the contactâ€™s outcome. In a hybrid complex between two towhee species in Mexico, Pipilo maculatus and Pipilo ocai, two major hybrid gradients provide natural replicates for comparison. However, genetic analyses demonstrate significant divergence between geographically separate parental populations of each species and divergence of populations within each hybrid zone. The two hybrid transects (TeziutlÃ¡n and Transvolcanic) are distinct and evidence suggests allelic introgression both across the species boundary and between the two transects. Habitat corridors for dispersal represent functional connectivity hotspots where the two transects meet. Both habitat connectivity and genetic differentiation between geographically disparate parental populations appear to influence the dynamics of gene flow across the hybrid gradients. In southern sympatric populations (Mt. Orizaba and Oaxaca) where morphological evidence for hybridization is scarce, opposing speciesâ€™ alleles appear to traverse through the hybrid zones rather than arising from cryptic local hybridization. These results illustrate the importance of environmentally mediated gene flow in the context of secondary contact as an important force influencing evolutionary trajectory.