Species pairs of whitefish (Coregonus sp.) found in postglacial lakes are used to illustrate the benefits of combining molecular and ecological approaches in studies of adaptive radiation. A detailed mitochondrial DNA phylogeographic analysis revealed that this species complex is composed of five major phylogenetic groups identifying races that survived the Pleistocene glaciations in distinct refugia. It also provided evidence for parallel evolution of sympatric ecotypes, involving bofh allopatric and sympatric origins. This strongly indicated the role of natural selection in driving their divergence. A comparative analysis of niche partitioning supported the hypothesis that the persistence of differential ecological opportunity throughout their ontogeny may be the selective force promoting the extent of specialization reached by whitefish ecotypes. The possibility that these same ecological processes are also responsible for determining the extent of their reproductive isolation was supported by a negative correlation between the extent of gene flow, estimated from microsatellite loci, and that of morphological specialization between ecotypes in different lakes. Previous experimental studies, however, revealed that embryonic mortality rates were 2 to 5 times higher in hybrid compared to pure crosses of ecotypes from distinct glacial races. This indicates that both genetic and ecological mechanisms may jointly act to determine speciation rate in whitefish. It is hoped that this study will not only stimulate further the interest of evolutionary ecologists for molecular genetics, but also that of molecularists for ecology. Promoting the fusion of such apparentiy remote fields of research may represent the most important achievement of molecular ecology as a discipline.