When habitat becomes fragmented, populations of species may become increasingly isolated. In the absence of habitat corridors, genetic structure may develop and populations risk reductions in genetic diversity from increased genetic drift and inbreeding. Deforestation of the Cerrado biome of Brazil, particularly of the dry forests within the Parana˜ River Basin, has incrementally occurred since the 1970s and increased forest fragmentation within the region. We performed landscape genetic analyses of Pfrimer’s parakeet (Pyrrhura pfrimeri), a globally endangered endemic to the region, to determine if forest fragmentation patterns were associated with genetic structuring in this species. We used previously generated satellite imagery that identified the locations of Parana˜ River Basin forest fragments in 1977, 1993/94, and 2008. Behavioral data quantifying the affinity of Pfrimer’s parakeet for forest habitat was used to parameterize empirically derived landscape conductance surfaces. Though genetic structure was observed among Pfrimer’s parakeet populations, no association between genetic and geographic distance was detected. Likewise, least cost path lengths, circuit theorybased resistance distances, and a new measure of least cost path length complexity could not be conclusively associated with genetic structure patterns. Instead, a new quantity that encapsulated connection redundancy from the 1977 forest fragmentation data provided the clearest associations with pairwise genetic differentiation patterns (Jost’s D: r = 0.72, P = 0.006; FST: r = 0.741, P = 0.001). Our analyses suggest a 35-year or more lag between deforestation and its effect on genetic structure. Because 66 % of the Parana˜ River Basin has been deforested since 1977, we expect that genetic structure will increase substantially among Pfrimer’s Parakeet populations in the future, especially if fragmentation continues at its current pace.