The first part (part A) of this thesis focuses on the establishment and development of microsatellite (SSR) DNA markers in Central European Coregonus. During this work, SSR markers for three different fish species (C. lavaretus, U. krameri and P. perryi) were developed (Chapters II-IV), whereby Chapter II represents preliminary steps for subsequent studies on Coregonus as followed in the second part (part B) of this thesis. Chapters II-IV of part B, therefore, deal with the introgression and potential hybridization of native forms of Coregonus sp. with an introduced Baltic species C. maraena, as well as putative mechanisms responsible for reproductive isolation. Additionally, morphological measurements and phenotypic characters were to some extent included. Hence, chapter II reveals the genetic structure of Coregonus populations sampled throughout Austria within particular lakes as well as the evaluation of genetic differentiation among native Austrian populations. Moreover, levels of introgression and hybridization were evaluated with support of simulated hybrid-populations. Subsequent chapters focus more specifically on ecologically based mechanisms that may result in a level of reproductive isolation of these two closely related taxa. Therefore, ecological niche differentiation such as different spawning times and places were investigated with the use of genetic markers. Chapter III describes the spatial distribution based on mitochondrial DNA data of larval and juvenile fish with regard to space and time in two Austrian lakes. Chapter IV centers on the spawning time of adult fish in one particular Austrian lake. Based on our results, however, the model that we propose is that there is restricted gene flow and thus restricted hybridization between the native and the introduced form, while complete admixture is impeded through ecological factors such as temporal segregation.