It is well known theoretically that gene flow can impede genetic differentiation between populations. In this study, we show that in a highly mobile bird species, where dispersal is well documented, there is a strong genetic and morphological differentiation over a very short geographical scale (less than 5 km). Allocation tests revealed that birds caught in one area were assigned genetically to the same area with a very high probability, in spite of current gene flow. Populations were also morphologically differentiated. The results suggest that the relationship between gene flow and differentiation can be rather complicated and non-intuitive.