Divergent habitat utilization and niche partitioning can cause high degrees of ecological specialization even in generalist species. For example, sex-specific specialization results in differential habitat use, which, if neglected in monitoring studies, can lead to biased estimates of population sizes. However, many widely used methods of population monitoring such as bioacoustical surveys of echolocating bats cannot take such demographic differences into account, due to methodological limitations. Here, we use ecological niche factor analysis (ENFA) to derive habitat suitability maps (HSMs) of male and female parti-coloured bat Vespertilio murinus using previously published radio-tracking data. The ENFA revealed that males and females were highly specialized and ecologically segregated. Accordingly, we found that significantly more high-quality habitats were available for males than for females, with no spatial overlap between sexes. The HSMs allowed us to estimate the skew in the distribution of the sexes in space. Our approach provides a way to estimate intra-species spatial segregation and consequently generate a more accurate prediction of effective population size and niche requirements of vulnerable species. This study also highlights the importance of making geographic and environmental data, as well as animal occurrence and movement data publicly available for the benefit of conservation efforts.