Species viability is strongly connected to the degree of gene flow within and among populations. Such genetic population connectivity may closely track demographic population connectivity or, alternatively, the rate of gene flow may change relative to the rate of dispersal. In this study, we have explored the relationship between genetic and demographic population connectivity using the Scandinavian brown bear as model species, due to its pronounced male dispersal and female philopatry. Our expectation, based on published demographic data, was that the philopatric females shape genetic structure locally whereas the dispersing males act as genetic mediators among regions. To test this, we used eight validated microsatellite markers on 1531 individuals sampled non-invasively during country-wide genetic population monitoring in Sweden and Norway from 2006 to 2013. First, we determined sex-specific genetic structure and substructure across the study area. Second, we compared genetic differentiation, migration/gene flow patterns and spatial autocorrelation results between the sexes both within and among genetic clusters and geographic regions. Our results indicated that demographic connectivity was not a reliable indicator of genetic connectivity. On larger geographic scales, among genetic clusters, we found no consistent difference in long term gene flow and estimated current migration rates between males and females. On smaller geographic scales, only females consistently displayed significant positive spatial autocorrelation, indicating male-biased small scale dispersal. An exception was displayed in one cluster, where males showed significant positive spatial autocorrelation, similar to the females. The Scandinavian brown bear population has experienced substantial recovery over the last decades; however, our results did not show any changes in the large scale population structure compared to previous studies, suggesting that an increase in population size and dispersal of individuals does not necessary lead to increased genetic connectivity. Thus, we conclude that estimates of both genetic and demographic connectivity should be performed so as not to misconceive the reality of wildlife populations.