The Strange-tailed Tyrant Alectrurus risora (Aves: Tyrannidae) is an endemic species of southern South American grasslands that suffered a 90% reduction of its original distribution due to habitat transformation. This has led the species to be classified as globally Vulnerable. By the beginning of the last century, populations were partially migratory and moved south during the breeding season. Currently, the main breeding population inhabits the Iberá wetlands in the province of Corrientes, north-east Argentina, where it is resident all year round. There are two remaining small populations in the province of Formosa, north-east Argentina, and in southern Paraguay, which are separated from the main population by the Parana-Paraguay River and its continuous riverine forest habitat. The populations of Corrientes and Formosa are separated by 300 km and the grasslands between populations are non-continuous due to habitat transformation. We used mtDNA sequences and eight microsatellite loci to test if there were evidences of genetic isolation between Argentinean populations. We found no evidence of genetic structure between populations (ΦST = 0.004, P = 0.32; Fst = 0.01, P = 0.06), which can be explained by either retained ancestral polymorphism or by dispersal between populations. We found no evidence for a recent demographic bottleneck in nuclear loci. Our results indicate that these populations could be managed as a single conservation unit on a regional scale. Conservation actions should be focused on preserving the remaining network of areas with natural grasslands to guarantee reproduction, dispersal and prevent further decline of populations.