Pleistocene glacial oscillations and associated tectonic processes are believed to have influenced the historical abundances and gradients of organisms in the Asia Northwest Pacific (ANP) Ocean. However, accumulating evidence indicates that factors shaping tempo-spatial population dynamics and distribution patterns of marine taxa vary with biogeographical latitude, pelagic behavior and oceanographic regimes. To detect what kinds of historical and contemporary factors affected genetic connectivity, phylogeographic profiles of littoral macroalga Sargassum horneri in the ANP were analyzed based on mitochondrial (Cox3) and chloroplast (rbcL) data sets. Five distinct clades were recovered. A strong signature of biogeographical structure was revealed (ФCT = 0.487, P < 0.0001) derived from remarkable differentiation in clade distribution, as clade I is highly harboured along Chinese marginal seas (Yellow-Bohai Sea, East China Sea and South China Sea), whereas clades II-V are discontinuously scattered around the main Islands of Japan. Furthermore, two secondary contact regions were identified along the south Japan-Pacific coastline. This significant differentiation between the two basins may reflect historical glacial isolation in the northwestern Pacific, which is congruent with the estimates of clade divergence and demographic expansion during the late Quaternary low sea levels. Analysis of molecular variance and the population-pair statistic FST also revealed significant genetic structural differences between Chinese marginal seas and the Japanese basin. This exceptional phylogeographic architecture in S. horneri, initially shaped by historical geographic isolation during the late Pleistocene ice age and physical biogeographic barriers, can be complicated by oceanographic regimes (ocean surface currents) and relocating behavior such as oceanic drifting.