The genus Salamandra encompasses six species with marked color pattern variations (yellow spots on black or primarily black or yellow) and reproductive strategies (viviparous and larviparous). This heterogeneity could be a consequence of habitat-specific adaptations, potentially related to the use of marginal ecological niches by some species or populations. This study investigated the habitat properties at 189 sites from the Iberian and Italian Peninsulas, northwest Africa, and the island of Corsica, where species of Salamandra are present: Salamandra algira, Salamandra atra, Salamandra corsica, Salamandra lanzai, and Salamandra salamandra. We used multivariate outlying mean index analysis to model species–environment relationships. The species showed differentiation in the habitat characteristics, and one group demonstrated specialization in high-elevation habitats (S. atra, S. lanzai). Our analyses also indicated that viviparous, primarily black phenotypes were associated with marginal habitats. By contrast, primarily yellow phenotypes were associated with habitats with structural properties similar to those used by typical (spotted-striped) phenotypes. These findings suggest complex regulatory mechanisms underlying the color variation in Mediterranean salamanders.