Mesotriton alpestris and the Apennine endemic Mesotriton apuanus are two recently recognized species characterized by distinct evolutionary histories, although their ecological differentiation has never been investigated in detail. In this study, we compared their ecological niches in northern Italy using Ecological Niche Models (MaxEnt) based on occurrence data from Trentino-Alto Adige (M. alpestris) and Liguria (M. apuanus). Models included climatic, topographic, and land-cover variables and showed fair-to-good predictive performance (AUC = 0.72–0.79). The ecological niche of M. alpestris was mainly driven by climatic and topographic factors, particularly annual mean temperature, precipitation, and slope exposure, whereas M. apuanus was more strongly associated with land-cover variables, especially deciduous forests, and precipitation. The comparison of response curves and variance partitioning highlighted different environmental relationships between the two species. Moreover, a symmetric background similarity test showed that niche overlap was significantly lower than expected by chance (D = 0.67, P ≈ 0.04), supporting the presence of ecological niche divergence. These findings suggest that the long-term evolutionary separation of the two taxa was accompanied by ecological differentiation, providing ecological support for their recent taxonomic distinction and contributing to a better understanding of adaptation processes in cold-adapted amphibians.