In sympatry, juvenile brown trout (Salmo trutta) usually occupy the shallow and most productive areas (littoral zone) of lakes, while juveniles of Arctic charr (Salvelinus alpinus) are found in deeper, less productive parts. In contrast, when Arctic charr juveniles occur in allopatry, they often occupy shallow littoral areas as well. Habitat segregation has traditionally been interpreted as a trade-off between predation risk and energy gain, while the segregation of these two species has been explained by brown trout being more aggressive and competitively superior to Arctic charr. We hypothesize, however, that the marked habitat segregation between the two species may also be due to differences in predator avoidance. Accordingly, we conducted several laboratory tests, using Arctic charr and brown trout as potential predators. Live fish of the same species were offered as prey, either as small charr only, small trout only, or both small charr and small trout together. Artificial shelters were then introduced to examine the avoidance ability of prey fish against predatory fish. Our results showed that under these circumstances, access to shelters strongly decreased mortality in juvenile brown trout, but had no effect on juvenile Arctic charr mortality. Thus, the habitat segregation shown by sympatric juvenile Arctic charr and brown trout in lakes may be a consequence of interspecific differences in predator avoidance.