Predatory fish can have a major impact on aquatic amphibian assemblages. Knowledge regarding the influence of habitat heterogeneity on predator-prey dynamics is extensive, but not much is published on how the habitat structure influences the co-occurrence of brown trout (Salmo trutta Linnaeus, 1758 morpha fario) and Fire Salamander (Salamandra salamandra (Linnaeus, 1758)). I examined the microhabitat distribution of larval salamanders relative to the presence of brown trout and stream morphology, hypothesizing that larval salamanders will increase their habitat use in the presence of trout to avoid predation. Fish and salamanders were sampled with an electroshocker in 62 instream habitat patches. In the stream zone populated by brown trout, larval salamanders avoided high-quality habitats such as pools, whereas they strongly preferred them in the fishless zone (their densities were ~10 times lower in pools than in riffles). Brown trout mainly occupied deeper pools. The co-occurrence of larval Fire Salamanders with trout suggests the presence of an effective predator-avoidance strategy. The predator-avoidance response and habitat-use pattern decreased interspecific overlap, leading to the use of different instream spaces. Heterogeneous habitats enable habitat partitioning between larval salamanders and brown trout, which means that the natural characteristics of streams promote coexistence between fish and amphibians.