Understanding the interplay of dispersal and how it translates into gene flow is key to understanding population processes, and especially so for endangered species occupying fragmented habitats. In migratory songbirds, there is evidence that long-distance movement capabilities do not translate well into observed dispersal. Our objectives were to (i) define the fine-scale spatial genetic structure in endangered black-capped vireos to characterize dispersal patterns and (ii) to correlate dispersal dynamics to overall population genetic structure using a simulation approach. We sampled 160 individuals over 2 years to (i) describe the fine-scale genetic structuring and (ii) used this information to model scenarios to compare with actual data on change in population structuring over a 100-year interval. We found that black-capped vireos exhibit male philopatry and restricted dispersal distances, relative to females. Our simulations also support a sex-biased dispersal model. Additionally, we find that fragmentation related changes in rates of dispersal might be a likely cause for increasing levels of population structure over a 100-year period. We show that restricted sex-biased dispersal can explain population structuring in this species and that changes in dispersal rates due to fragmentation may be a continuing threat to genetic viability in this species.