The European whitefish, Coregonus lavaretus (L.), is a highly polymorphic species consisting of several distinct ecotypes or forms. In the Koitajoki watercourse, south-eastern Finland, there exists a pair of indigenous sympatric whitefish ecotypes with distinct gill raker numbers. In the watercourse, supplemental stocking was initiated in the 1960s to compensate recruitment failure of whitefish caused by water level regulation for hydroelectric purposes. We investigated the genetic differentiation and possible hybridization between the two forms using 21 microsatellite loci and by assessing the temporal changes in the distribution of gill raker numbers. The distribution of gill raker number shifted from bimodality to trimodality in less than 15 years during the 1980s and 1990s, implying putative hybridization of these forms. Significant genetic differentiation was found between the two forms (F-ST = 0.034). In addition, Bayesian inference of population structure as well as a discriminate analysis of principal components (DAPC) identified two genetic clusters largely coincident with these forms. A high degree of genetic admixture was found in phenotypically intermediate individuals, which also differed slightly from the indigenous forms as indicated by the DAPC scatterplot. Taken together, the results suggest that human actions such as stockings and water level regulation are the most likely factors contributing to the reduction of reproductive isolation between the sympatric whitefish forms.