Altitude can profoundly influence the distribution of mammals, although the majority of studies of altitudinal impacts on distribution and abundance examine large-scale effects in mountainous environments. We investigate the potential for altitudinal effects on within-habitat distribution in common and soprano pipistrelle bats (Pipistrellus pipistrellus and Pipistrellus pygmaeus) over relatively small scales on the Isle of Man, an island with a maximum altitude of 620 m above sea level. While we found no differences in habitat or altitude usage between the two species, both showed a sharp decline in activity with small increases in altitude within all habitats. This decline was steepest in deciduous and conifer woodland, and more gradual in arable land and heath-land. Activity also declined more quickly with increasing altitude in the centre of habitats compared with the edge, and where water was present compared with where water was absent. We suggest that altitude may limit distribution independent of habitat, and thus is an important factor to take into account, in combination with habitat, when designing mammalian conservation strategies.