The Montagu’s harrier (Circus pygargus) is a semi-colonial raptor species widely but patchily distributed across the Palearctic region with recorded cases of philopatry and presence of extra-pair copulation. In order to assess Montagu’s harrier spatial genetic structure and contemporary gene flow, we developed 16 new microsatellite markers using 454 pyrosequencing. Genotypes of 117 chicks sampled in a 200 × 300 km farmland area in Central Western France were analyzed to characterize genetic polymorphism at each locus and regional and fine-scale genetic structure. Fourteen markers were found polymorphic, with a number of alleles ranging from 3 to 11. The expected and observed heterozygosities ranged from 0.36 to 0.856 and from 0.35 to 0.868, respectively. A single genetic unit was found at the regional scale with higher genetic similarity observed at a small spatial scale (up to 10 km). Our results are consistent with overall large-scale juvenile and adult dispersal together with small-scale male philopatry. Cross-species amplification of this set of microsatellites makers has been successful in two closely related harrier species: the marsh harrier (Circus aeruginosus) and the Hen harrier (Circus cyaneus) for which 14 and 12 markers were polymorphic, respectively. These new microsatellite markers could be used to study the population genetic structure, contemporary gene flow and parentage analyses in these three species and to conduct microsatellite-based demographic inferences on the Montagu’s harrier.