We analysed the mitochondrial control region sequences of 150 Ryukyu robins (Erithacus komadori) from five migratory and three sedentary populations. E. komadori is endemic to the subtropical Asian islands, is well differentiated among populations in morphology and migratory behaviour within its narrow habitat range, and is ideal for examining the effects of altered migratory habits on population differentiation. Maximum-likelihood analysis among the haplotypes resulted in the generation of a single tree in which two phylogenetic clades corresponding to the two subspecies were evident. Within the northern lineage, three distinctive subgroups of populations (one migratory and two sedentary groups) were observed by population genetic analysis. The migration-related wing morphology and molecular data were then compared among groups. The wing shape of the northern lineage was significantly more pointed than that of the southern sedentary lineage, and they were exclusively discriminated from each other. The difference was not so apparent between the sedentary and migratory groups within the northern lineage, suggesting that the present northern subspecies is primarily a migratory lineage. The different migratory behaviours of the robin played an apparent role in maintaining the genetic structure at two different levels — one between the southern and northern lineages and the other between the sedentary and migratory groups within the northern lineage. While gene flow had long been maintained among the islands occupied by migratory individuals, migrants have been unable to contribute to the gene pool of the sedentary populations despite passing through the breeding range of such populations twice each year.