The Montagu’s harrier (Circus pygargus) is a long-distance migratory raptor, breeding in Europe and Western Asia and wintering in sub-Saharan Africa. The population of the species has declined in Europe during the twentieth century, and Montagu’s harrier is red-listed in many European countries as declining or threatened. The main aims of the study were to evaluate the genetic diversity of European breeding populations and estimate the genetic differentiation among them, using polymorphism in the hypervariable domain of the mitochondrial control region. We analysed 158 individuals from central Spain, Germany, the Czech Republic and Poland. The results indicated high genetic diversity in the European breeding population, probably reflecting the large population size of the species. However, we found decreased genetic variability in the breeding population of Germany. Among the 18 identified haplotypes, 2 were of high frequency. There was no clear connection between the position of the haplotype in the genealogy and its geographical distribution. Genetic structure was weakly pronounced (H ST = 0.053, P < 0.001). SAMOVA indicated the presence of three genetic groups: The first group consisted of samples from central Spain and northeastern Poland, the second from southern Poland and the Czech Republic, and the third group separated samples from Germany from the other regions. Genetic differentiation between pairs of groups was low, suggesting a low level of philopatry and a high dispersal ability of Montagu’s harrier.