AbstractThe Atlas flycatcher (Ficedula speculigera) is a poorly studied species in an otherwise thoroughly studied species complex. In this study I attempt to reconstruct the evolutionary history of this species, I look for possible traces of introgression, I test whether there is contrasting patterns of polymorphism and divergence at autosomal and Z-linked genes as has been found in other flycatcher species, and finally whether the Atlas flycatcher show reduced genetic variation which would be expected due to recent habitat fragmentation. To address these problems I used multilocus sequence analysis, with loci from both autosomes and Z-chromosomes, and compared these with previously published sequences from two other species, the pied flycatcher (F. hypoleuca) and the collared flycatcher (F. albicollis). Finally, phenotypic measures of the Atlas flycatcher were compared with measures of these other two species. The results appear consistent with a scenario in which an ancestral flycatcher species became isolated in different refugia, presumably around the Mediterranean Sea, at the onset of the Pleistocene glaciations and diverged into the present species. I found no traces of introgression between the Atlas flycatcher and any of the two other species. Further, the Atlas flycatcher showed reduced variation at Z-linked loci compared to autosomal loci, which may indicate a complex demographic history or possibly selection. The Atlas flycatcher also showed high variation compared to the other two species, and therefore seems to have a rather large effective population size.