Forces driving the evolution of reproductive isolation among natural populations, as well as the mechanisms involved to maintain it, are still poorly understood. Because sympatric fish ecotypes mainly differ in phenotypic traits associated with occupying distinct trophic niches, it is generally believed that reproductive isolation is mainly driven by ecological divergent selection, excluding genome incompatibility as a basis for postmating isolation. We did cross experiments between dwarf and normal ecotypes of lake whitefish (Coregonus clupeaformis Mitchill) originating from distinct glacial refugia to test the hypothesis that their geographical isolation during the Pleistocene may have led to sufficient genetic divergence for the development of reproductive isolation between them before their secondary contact. Similar fertilization success in pure and hybrid crosses indicated the absence of gametic incompatibility between the two ecotypes. In contrast, daily embryonic mortality rates were 2.4–4.7 times higher in reciprocal hybrid crosses compared to pure crosses, which supports our working hypothesis. These results, along with previous morphological and population genetic studies, indicate that both genetic and ecological mechanisms may jointly act to promote speciation among northern freshwater fish ecotypes.