Interspecific competition affects population dynamics, distributional ranges, and evolution of competing species. The competitive exclusion principle states that ecologically similar species cannot coexist unless they exhibit niche segregation. Herein, we assess whether niche segregation allows the coexistence of Crocidura russula and C. suaveolens in southwestern Iberia and whether segregation is the result of current (ecological effect) or past (evolutionary effect) competition. We performed an annual live-trapping cycle in the two main habitats of the Odiel Marshes Natural Reserve (OMNR), the tidal marsh and the Mediterranean forest, both in syntopic (i.e., where both species co-occur) and allotopic (where only one of the two species occurs) sites within this Reserve. We modeled the presence–absence of each species in both habitats and sites by generalized linear mixed models. The coexistence of both species was favored by spatial and temporal niche segregation. Crocidura suaveolens was restricted to tidal marsh and did not occupy Mediterranean forest, even when C. russula was absent. We interpret this to be the result of competition in the past triggering an evolutionary response in C. suaveolens towards its specialization in tidal marsh. Moreover, the specialist C. suaveolens currently is outcompeting C. russula in tidal marshes, reversing the dominance pattern observed elsewhere. The degree of co-occurrence between both species in syntopic sites was low, as they showed inverse dynamics of seasonal abundances. Interspecific competition leading to habitat specialization favors the coexistence of these ecologically similar species.