The study of the genetic structure of the coregonid populations in the eastern part of the Gulf of Finland based on 30 enzyme loci revealed the poor differentiation of the majority of the samples from the Coregonus lavaretus L. populations that were caught close to the mainland’s shoreline (D N = 0.000–0.005). The genetic differences between the anadromous whitefishes of the Gulf of Finland and the populations of whitefishes from the Ladoga and Onega lakes also turned out to be minimum. The sea populations of the species that populate the open part of the Gulf of Finland near the Russian islands have significantly diverged genetically from the main pool of the populations of the Gulf of Finland (D N = 0.018–0.037). The presence of the CK-Al,2*c allele with a high frequency (p ≥ 0.5) in the gene pool of the sea whitefish implies the probable origin of the island populations from a separate evolution lineage of whitefish of Western Europe or a taxon of complex evolution origin as a result of the introgressive hybridization between different species of coregonids. The phylogenetic closeness and common character of the origin of all the investigated samples of the vendace Coregonus albula L. from the Gulf of Finland and the Ladoga and Onega lakes are supported by the low values of the genetic distances between them (D N = 0.000–0.008).