The white wagtail (Motacilla alba) was a puzzling species for biologists over decades. Marked plumage differences of the nine subspecies and observations that several subspecies pairs coexist side-by side where their ranges overlap made scientists think that these are quite different entities, evolutionarily speaking, even different enough to call some of them a separate species. It was therefore expected that genetic markers should reflect patterns of phenotypic differentiation at some degree - as it commonly works for many other species. Surprisingly, genetic markers failed to differentiate between plumage clusters - and it does not matter whether you take a couple of mitochondrial loci, a bunch of microsatellites or tens of thousands of single nucleotide polymorphisms scattered throughout the genome. Such systems as wagtails are not just interesting because they do not fit our expectations about patterns and processes of evolution and we naturally want to know why. They also represent early stages of speciation continuum, when vast majority of the genome remains relatively undifferentiated with exception of few key genomic regions involved in build-up and maintenance of reproductive barriers - and by studying these genomic regions, their association with phenotypic traits and the mechanisms that maintain their integrity we can learn how and why populations evolve towards different species. For my master, PhD and shortly after I was studying a hybrid zone between two subspecies - alba and personata - trying to illuminate these questions.