Although widespread in Europe, the white-throated dipper Cinclus cinclus has a fragmented distribution in the Iberian Peninsula. We investigated whether Iberian dipper populations are genetically differentiable by assessing a fragment of the cytochrome b gene in birds from 11 geographical areas encompassing 48 Iberian rivers. Four population groups North, Centre, East and South were differentiated a priori on the basis of geographical criteria. Genetic differences between these groups explained 35.9% of the total variation. Eight new haplotypes have been recorded for this species. The most abundant haplotype (H3) was shared by 75.8% of the birds and was found in all areas. The second most abundant haplotype (H10, 17.6% of individuals) was present in three areas: two in the southern mountains and one in central Iberia. The third most abundant (H5, 4.8% of birds) occurred only in central Iberia. Southern populations are genetically distinct from the others.