In mountain ecosystems, the persistence of species increasingly depends on the maintenance of functional connectivity under the dual pressures of climate and land-use change. “Sky island” species such as the mountain hare (Lepus timidus) are particularly vulnerable, being restricted to high-altitude cold-climate habitats. Meanwhile, generalist and expanding species like the  European hare (L. europaeus) may further threaten their persistence through interspecific competition. Despite growing concern about biodiversity in mountain regions, fine-scale assessments of landscape connectivity and its drivers remain limited. We investigated how environmental and anthropogenic variables affect functional connectivity in both the mountain hare and the European hare in the French Alps, and how interspecific interactions might modulate connectivity patterns. We used machine-learning landscape genetics approaches with microsatellite data from 1564 mountain hares and 1143 European hares sampled across the French Alps. This allowed us to assess the effect of 13 landscape variables at multiple spatial scales on gene flow and validated results across five sub-areas to test for regional consistency. While the genetic structure was weak in both species, connectivity patterns were species-specific and opposite, shaped by distinct environmental variables and the interspecific competition for the mountain hare. For example, elevation increased gene flow in the mountain hare but limited it in the European hare. Connectivity maps confirmed contrasted spatial patterns: mountain hare corridors were confined to high elevations, while European hare connectivity concentrated in lowlands and valleys. Interspecific competition may further restrict mountain hare movement by limiting access to lower-elevation corridors increasingly dominated by the European hare. Our findings highlight contrasted landscape permeability between a cold-adapted species and a generalist competitor. The expansion of anthropized areas in Alpine valleys may exacerbate connectivity loss in mountain hares. Conservation strategies should prioritize the maintenance of high-altitude corridors to support climate-driven range shifts and reduce competition pressure.