Aim: In theory, long-distance dispersal (LDD) outside a species’ range contributes to genetic divergence. However, previous studies have not discriminated this process from vicariant speciation in migratory bird species. We conducted an integrative phylogeographic approach to test the LDD hypothesis, which predicts that a Japanese migratory bird subspecies diverged from a population in the coastal region of the East China Sea (CRECS) via LDD over the East China Sea (ECS). Location: East Asia Taxon: Brown Shrike (Lanius cristatus) Methods: Both a haplotype network and a multi-locus gene network of its three subspecies were reconstructed to examine from which continental population the Japanese subspecies diverged. A species distribution model (SDM) for the Japanese subspecies was constructed using bioclimatic variables under the maximum entropy algorithm. It was projected to the climate of the last glacial maximum (LGM) to infer the candidate source area of colonisation. A migratory route of the Japanese subspecies, which possibly reflects a candidate past colonisation route, was tracked by light-level geolocators. Results: Molecular phylogenetic networks suggest that the Japanese subspecies diverged from a population in the CRECS. The SDM inferred that the emerged continental shelf of the ECS and the present CRECS were suitable breeding areas for the Japanese subspecies during the LGM. A major migratory route for the Japanese subspecies was inferred between the CRECS and the Japanese archipelago across the ECS. Main conclusions: Our integrative approach supported the LDD hypothesis for divergence of the Japanese subspecies of the Brown Shrike. Shrinkage and expansion of the ECS may have been responsible for successful colonisation and isolation of the new population. Vicariance was inferred for divergence of the subspecies in the northeast Asian continent from the Japanese population. Our framework provides a new phylogeographic scenario in this region, and discriminating LDD and vicariance models should improve our understanding of the phylogeographic histories of migratory species.