Numerous studies have highlighted a major role of isolation by both geographic distance and current landscape resistance in controlling bird population genetic differentiation. However, the importance of past landscape features or landscape temporal stability in shaping population genetic structure remains undervalued, particularly in birds. We assessed the role of isolation by landscape resistance – derived from current landscape attributes and measures of landscape stability –, in comparison to geographic isolation, as drivers of genetic differentiation of the Iberian bluethroat (Luscinia svecica azuricollis), a migratory bird whose populations breed in fragmented and dynamic landscapes affected by land use change. First, we characterized bluethroat genetic structure using microsatellite genotypes and evaluated genetic distances. Then, we built species distribution models using as a predictor a time series (two decades) of values of the Normalized Difference Vegetation Index as proxies of recent past landscape stability and current landscape features to ultimately generate landscape resistance values through different functions. Finally, we used maximum‐likelihood population effects models to evaluate the relationships between genetic distances and both geographic and landscape resistance distances. We found a genetic structure of four clusters in the Iberian bluethroats populations, as well as a high level of genetic differentiation. Genetic structure was better associated with landscape resistance, rather than with geographic distance. The highest values of habitat suitability corresponded to areas where vegetation remained mostly stable during the two decades prior to bird surveys, with low annual precipitation and spring temperature, being the relationship between gene flow and presence of intervenient habitat among populations linear or quasi‐linear. Our results suggest that conservation policies and land management practices that promote the maintenance of semi‐open pasture‐shrub mosaics (e.g. through extensive livestock grazing) can strongly benefit Iberian bluethroat populations, improving gene flow and population connectivity.