Wing shape plays a major role in determining the aerodynamics and performance of avian flight. Intraspecific variation in wing shape reflects different migratory strategies or distances between breeding and wintering areas. Differences in the wing morphology and genotypes between coastal and inland breeding populations of the Reed Warbler in Croatia were studied. A total of 105 adult birds were measured, while blood samples were taken from 59 individuals. The results showed that the two geographically close populations of Reed Warblers differ in wing morphology, with birds from the inland population having more pointed and more slotted wings than those from the coastal population. There was a slight but significant difference in microsatellite allele frequencies between the two populations (FST = 0.015), suggesting that gene flow between the two populations is partly restricted. The differences in wing morphology imply that the two populations use different migratory routes and/or winter in different areas. Consequently, this migratory pattern may have influenced the contemporary genetic differentiation of the two populations.