The aim of our study was to find suitable molecular markers for genetic studies of the population of Montagu's harrier Circus pygargus. We used the crossspecies amplification strategy to test the usefulness of 24 primer pairs, amplifying the microsatellite loci of several other members of Accipitridae. The analysis was performed on 139 Montagu's harriers from breeding populations in Spain and Poland. We found an amplification success of 50%; however, the level of polymorphism in cross-amplified microsatellites was low, especially in terms of heterozygosity. We did not find significant differences in genetic variability, estimated based on microsatellite markers, between breeding populations from Spain and Poland. The level of genetic differentiation between these two populations was low (F_ST = 0.016), although significant. An analysis of genotypes of nestlings in 10 nests suggested one case of extra-pair paternity.