The question of whether migratory behavior can promote speciation has been studied in subspecies with different migration pathways to distinct wintering grounds. But another mechanism by which migration can promote speciation is via loss of migration, when a population splits from the migratory population and becomes permanently sedentary. Hundreds of migratory species also have populations (or subspecies) that are sedentary (partial migration), and this may be an intermediate stage of the speciation process. We studied the phylogeographic history of the Fork-tailed Flycatcher (Tyrannus savana), a species composed of a long distance migratory subspecies (T. s. savana) that breeds in southern South America and migrates during the non-breeding season to northern South America, where it coexists with three other sedentary subspecies (T. s. monachus, T. s. sanctaemartae and T. s. circumdatus). Based on mtDNA sequences and 41458 SNPs obtained through Genotyping by Sequencing, we find evidence for a recent divergence associated to loss of migration. Our results show that mtDNA was monomorphic and genetic distances between subspecies based on GBS were low. We found low genetic diversity in the sedentary subspecies in comparison to the migratory subspecies and population assignment analyses cluster all three sedentary subspecies as one group apart from the migratory subspecies. Estimations of gene flow are low, suggesting reproductive isolation between all subspecies. Our results suggest that loss of migration promotes reproductive isolation. Further studies aiming to understand how migratory species respond to changes in resource distribution can shed light into the triggers and ubiquity of this phenomenon.