The Semi-collared flycatcher (Ficedula semitorquata) is a member of the black-and-white flycatcher species complex. It is poorly studied, rare, and is currently classified as “near threatened”, in the IUCN red lists of threatened species. The Semi-collared flycatcher has a patchy distribution in Europe and part of the Middle East. In this study, I analyzed sequence variation at nuclear loci of Semi-collared flycatchers, and compared the patterns found with those of three other black-and-white flycatcher species, the Pied (F. hypoleuca), Collared (F.albicollis) and Atlas flycatchers (F. speculigera). Genetic variation was found to be relatively high, compared to the other three flycatcher species and there were no signs of inbreeding. All four flycatcher species had less variation at Z-linked loci compared to autosomal loci. A comparison showed that all species combinations had fewer shared polymorphisms and more fixed substitutions at Z-linked than at autosomal loci. Selective sweeps on the Z-chromosome during the evolutionary history of these species is likely to have contributed to this pattern. A mismatch distribution showed signs of a recent population expansion in all four species, and a phylogenetic reconstruction confirmed a relatively deep split and that each species is monophyletic. This study supports the classification of the Semi-collared flycatcher as a separate species. Even though no signs of a small population size are found here, it is important to keep monitoring this bird, since it has gone through several declines across Europe during the last decades. Much of the decline is probably due to habitat destruction, so it is important to retain old forest in the habitat of the species.