Significant demographic fluctuations can have major genetic consequences in wild populations. The Lesser Kestrel ( Falco naumanni ) has suffered from both population declines and range fragmentation during the second half of the 20th century. In this study we analysed multilocus microsatellite data to assess the genetic structure of the species. Our analysis revealed significant genetic structuring of Lesser Kestrel populations, not only at cross-continental scale, but also regionally within Central and Eastern (CE) Mediterranean. We detected signs of genetic bottlenecks in some of the peripheral populations coupled with small effective population sizes. Values of genetic differentiation among the largest populations were low, albeit significant, whereas the small peripheral CE Mediterranean populations showed higher levels of differentiation from all other populations. Gene flow levels were relatively low among the discontinuously distributed populations of the CE Mediterranean region. We argue that the observed spatial genetic structure can be attributed at some level to the past demographic decline experienced by the species. Finally, we identify management units in the region, and inform the design of conservation actions aiming at the increase of population sizes and dispersal rates among peripheral populations.