A large amount of world’s species diversity is the result of adaptive diversification to heterogeneous environments. Such species are reproductively isolated from each other by ecologically-based post zygotic isolation or mate choice. Changing environments can cause the breakdown of genetic isolation between such species. It has been shown that a loss of environmental heterogeneity can lead to fusion of species, on the other hand interspecific hybridization can under some circumstance contribute to increase biodiversity. To measure extent of genetic differentiation between two sympatric whitefish species of Lake Lucerne, we performed a quantitative sampling along an ecological gradient. Instead of the previously described known two species we found three genetically differentiated species along the gradient that further differ in morphology and life-history traits. The newly discovered species is genetically intermediate between the two previously known species but distinct from both. We discuss alternative hypothesis for its origin including the possibility that the recent environmental changes led to hybrid speciation and we discuss the effect of changing environmental conditions on the interaction between gene flow and selection and on the conservation of species.