Molecular phylogeography is an important sub-discipline of biogeography, which utilizes the molecular biological techniques to reconstruct the phylogenies of organisms at intra-species and inter-species levels, thus trace the evolutionary history and understand the historical nature of the biota. The neutral and coalescent theories provide theoretical framework for the phylogeographic studies. Mitochondrial DNA and microsatellites are most broadly used genetic markers. Recent advance has been made for birds in Europe and North America. These studies have revealed that that the various spatial distribution patterns and the centers of origin in the species-specific level, and identified different phylogeographic patterns either as the result of vicariance or dispersal. Moreover, differentiation on the migration behaviors between avian species has been recognized as the considerable factor in influencing the phylogeographic patterns. Compared with these two regions, avian phylogeography in China is newly started and more comparative phylogeographic studies are required for different geographical regions and species. Meantime, the usage of next-generation sequencing methods will potentially accelerate our understanding of avian phylogeography in the near future.