Dispersal constitutes one of the main processes that shape population genetic structure and dynamics. Combining a capture-mark-resighting methodology and molecular genetics analyses, we studied the natal dispersal behaviour of House Wrens (Troglodytes aedon bonariae) inhabiting a naturally fragmented habitat in south temperate Argentina. Based on data collected over 12 breeding seasons (2005–2016), we tested if males and females differ in natal dispersal behaviour at different spatial scales. At local scale (within study sites), both resighting of banded individuals and genetic analysis showed that females dispersed greater distances than males. At a broader spatial scale (between study sites) resighting of banded individuals could not verify that females were the dispersing sex since long-distance dispersal was rare. However, genetic analyses revealed paradoxical evidence: while the females of populations separated by more than 5 km showed slight but significant genotypic differences among them, males showed genetic differences at a greater distance (> 16 km). Given that genetic analyses can provide evidence of both historical and present-day dispersal the observed genetic differentiation does not necessarily imply that the sex dispersal pattern is reversed at a regional scale. We propose that females have a higher probability of acquiring a partner/territory at closer distances due existing male-biased population sex ratio caused but higher female mortality. Also, although males are less likely to disperse, when they do, they must travel greater distances to find a suitable territory or mate. Such movements would prevent the occurrence of genetic differences among male populations.