Brown and polar bears have become prominent model organisms in phylogeography, but previous phylogeographic studies were geographically restricted, or relied largely on maternally inherited mitochondrial DNA (mtDNA). The male-specific Y chromosome, a natural counterpart to mtDNA, has remained under-explored. Although this paternally inherited chromosome is indispensible for integrative analyses of phylogeographic patterns, technical difficulties have hampered its application in most mammals. We developed novel Y-chromosomal markers from the polar bear genome, and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390 kb-long Y-chromosomal fragment from published male ursine genomes. Contrary to well-established mtDNA patterns, we found (i) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, (ii) male-biased gene flow across continents and on phylogeographic time scales, and (iii) male dispersal that links the enigmatic Alaskan ABC-islands population to mainland brown bears. MtDNA-based studies have thus overestimated population structuring, due to female philopatry and the homogenizing effect of male-biased gene flow Our findings highlight the importance of analysing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history and that mtDNA-based phylogeographic studies of many mammals should be re-evaluated.