Hybridization between genetically divergent populations is common in nature. By comparing the rate of gene flow throughout the genome, loci that impede genetic mixing, and therefore underlie reproductive isolation, can be identified, providing key insights into the process of speciation. In a previous issue of Molecular Ecology, Geraldes et al. (2008) report the geographical distribution of Y chromosome lineages in wild populations of rabbits from across the Iberian Peninsula and southern France. Y chromosomes showed a high level of differentiation between rabbit subspecies on either side of a hybrid zone, despite clear evidence for gene flow at other loci. This provocative result suggests a role for the Y chromosome in reproductive isolation, and adds to a growing list of nascent species with mosaic patterns of differentiation across their genomes.