The Northern Andes, acting both as barrier and corridor, exert strong influence in Neotropical biodiversity. Still, the diversification of foothill taxa inhabiting ecotonal zones between lowland rainforest and montane environments in this region remains poorly understood. We investigated evolutionary patterns in Eutoxeres aquila, a hermit hummingbird distributed across Central America, the Chocó, and both Andean slopes. Using mitochondrial DNA (ND2, cytb), morphometrics, resistance surface analyses, and ecological niche models, we examined the roles of topography, connectivity, and climatic oscillations in shaping lineage divergence. Phylogenetic analyses of 59 individuals revealed two major E. aquila clades: (i) eastern slope–upper Magdalena and middle Magdalena–Tamá, and (ii) western slope–Chocó–Antioquia and Panama. Divergence from E. condamini occurred ~4.0 Mya, while crown diversification began ~1.6 Mya, coinciding with Pleistocene climate cycles. The Panama lineage diverged ~0.6 Mya, suggesting post-Isthmus dispersal. Morphometric analyses of 66 specimens showed significant bill shape differentiation among regions, broadly consistent with genetic structure. Ecological niche projections indicated expanded connectivity during the Mid-Holocene and LGM, but contraction and fragmentation during the LIG, with ~227,500 km² of long-term climatic stability concentrated mostly in Amazonia and the Chocó. These results highlight recurrent isolation and reconnection of mountain environments as key drivers of foothill diversification and emphasize the importance of ecotonal taxa for understanding Andean evolutionary processes.