Human-induced hybridization between previously allopatric species deserves special attention from conservationists. The European whitefish (Coregonus lavaretus), native fish species in Poland, hybridizes with another coregonid fish—peled (Coregonus peled) due to artificial fertilization in the hatcheries. The latter species is native to Siberian waters and was introduced into Poland in 1966. The offspring of these two species are fertile, and interspecific hybrids have been shown to be present in certain Polish lakes. In this study, we estimate the level of peled introgression into the whitefish gene pool and verify the presence of pure whitefish populations in the four Polish lakes. Genetic analysis of 12 microsatellite loci and ITS 1 (internal transcribed spacer 1) fragment sequences revealed limited introgression. Bayesian admixture analysis showed that only one lake harbored an admixed population. All six admixed individuals possessed European whitefish mtDNA haplotypes. This study is the first comprehensive investigation of whitefish genetic diversity in Poland and revealed very limited introgression of peled. Obtained results showed that pure whitefish populations are still present in Poland and represent appropriate source for supportive breeding programs.