Abstract The implementation of effective and appropriate protection actions is frequently hindered by lack of thorough knowledge on species ecology especially in the case of endemic, vulnerable and elusive species. Using a recently updated and unpublished dataset describing the spatial distribution of the Pyrenean desman (Galemys pyrenaicus) in its northern range (French Pyrenees), an Ecological Niche Factor Analysis (ENFA) was conducted to provide a quantitative estimate of local habitat use by this endangered semi‐aquatic mammal. A comparative approach was used to investigate potential differences in habitat use among the three main hydrological regions of the French Pyrenees. The Pyrenean desman was identified as a marginal and specialist species concerning the selection of its local habitat in the French Pyrenees. Key habitat variables corresponded mainly to river‐bed characteristics (i.e. high heterogeneity of shelters and river substrates, fast flowing water facies, low amounts of fine sediment) and river‐bank characteristics (i.e. high proportion of rocks, low proportion of earth). A difference in habitat selection between the three hydrological regions of the French Pyrenees was also highlighted. A decrease in marginality and specialization from west to east as well as differences in habitat variables driving the ecological niche of the Pyrenean desman and its range suggested a spatial structure in desman populations regarding local ecological factors. These results stress the importance of effective and sustainable river management for the habitat quality of this endangered species and also demonstrate the importance of taking into account the variability in habitat preferences that can exist between geographically distinct populations. This finding has important implications for conservation planning that should thus be conducted at the population level instead of the traditional species level in order to target the specific needs of each hydrological region. Copyright © 2016 John Wiley & Sons, Ltd.
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