1. Conservation priorities are set on the basis of existing knowledge of the species concerned. Identification of cryptic species within former single taxa may significantly change the perspective on distribution and abundance which, in turn, might impact the species? conservation status. 2. In the 1990?s it was discovered that one of the most abundant bat species in Europe actually consists of two cryptic species, P. pipistrellus and P. pygmaeus. We systematically recorded echolocation calls from both species along road transects driven across Switzerland. Subsequently, we have used presence data obtained to analyse the species? habitat selection and respective ecological niches by GIS-modelling and by discriminant analysis. 3. Habitats mostly associated with P. pygmaeus presence are wide rivers and lakes, human settlements and open woodland habitats. P. pygmaeus is patchily distributed and only occurs in its optimum habitats, i.e. in areas characterized by the simultaneous presence of all habitats mentioned above. 4. P. pipistrellus has similar habitat preferences, but unlike P. pygmaeus, it is very tolerant with regard to deviations from its optimal habitat. The overall niche of P. pipistrellus encompasses nearly the entire global habitat availability. In contrast, the niche of P. pygmaeus is narrow and mostly included in one end of the niche of P. pipistrellus. 5. Due to its wide distribution and abundance P. pipistrellus sensu lato was ranked «not endangered» in Switzerland. In this study we found P. pipistrellus to occur in a 30-fold higher abundance than P. pygmaeus. However the rarity of P. pygmaeus and its restricted distribution significantly change the conservation status of this cryptic species. Extrapolated habitat suitability maps help to focus conservation efforts to protect important hunting areas (i.e. riparian woodlands) in regions with highest probability of occurrence. 6. Synthesis and applications. The present example points out that conservation status attributed to taxa encompassing sibling species may be misleading and needs to be changed constantly according to scientific advances. Progress in systematics will spawn more cryptic species in the near future. Ecological studies are required to assess their environmental requirements and provide the necessary baseline information for appropriate conservation.