Citation: Mehner, T., M. Emmrich, and P. Kasprzak. 2011. Discrete thermal windows cause opposite response of sympatric cold-water fish species to annual temperature variability. Ecosphere 2(9):104. doi:10.1890/ES11-00109.1Abstract. Cold-water fish populations in lakes are predicted to be most vulnerable to global warming due to their geographical isolation and their requirement for habitats with low temperatures. In contrast, higher fisheries catches of cold-water species often correlate with warmer winter and spring temperatures. Mechanistic understanding of the relationships between annual temperatures and population densities can only be achieved by integrating physiology and behavioral ecology of the focal species, an approach that has so far not been applied to freshwater fish populations. We took advantage from a unique biological system, the coexistence of two cold-water Coregonus species in a deep lake. These fish species show discrete thermal windows (4-58C vs. 7-98C) and life histories (spring-vs. autumn-spawning). We analyzed short (6-11 years) time series of pelagic fish densities obtained by hydroacoustics and trawl catches, their zooplankton prey densities, and water temperature in Lake Stechlin (Germany). Young-of-year fish densities increased after warm winters. In contrast, densities of juveniles and adults were correlated with metalimnetic June temperatures, but an opposite response direction of the sympatric species was caused by their discrete thermal windows. Densities of the species with a 4-58C thermal optimum increased in years with warm June, whereas densities of the other species with a 7-98C optimum declined in these warm years. The occupied depths of both populations at night shifted towards less suitable water temperatures if densities of the competing species increased, suggesting interactive niche segregation. Therefore, growth of fishes may be reduced and hence mortality increased by additional metabolic costs induced by occurrence in layers outside of the metabolic optima. Temperature-driven inter-and intra-specific competition in the metalimnetic layer may cause a complex response of cold-water fish assemblages in lakes to warming. More approaches testing the relative performance of interacting species are needed to improve predictions on the consequences of global change on lake ecosystems.