The Izu Islands of Japan are a geographically young volcanic archipelago nearer to the mainland than other islands used in speciation studies, such as the Galapagos Islands of Ecuador. On the Izu Islands, birds are likely to have undergone recent colonization and trait diversification. Three morphological groups of Varied Tits, Poecile varius, breed on the islands. The varius group, which has the smallest body size and is the same as that found on the mainland, breeds on the northernmost island (closest to the mainland). The namiyei group, which has an intermediate body size, breeds on two or three central islands, and the owstoni group, which has the largest body size, is found on several southern islands. To infer the gene flow ranges and colonization processes of Varied Tits with such obvious trait polymorphisms among the Izu Islands, we analyzed the genetic population structures of these three morphological groups. In genetic analysis of all samples, individuals were first divided into cluster A, which was composed of individuals from Kohzu Island (a central island) from the namiyei group, and cluster B, which was composed of individuals from mainland sites and other islands (excluding Kohzu and Niijima). The genetic characteristics of individuals from Niijima may indicate a recent gene flow event between clusters A and B. Individuals from the owstoni group were genetically similar to varius group individuals, despite the large distance between the breeding areas of these two groups. The second step of our analysis used samples from cluster B. These samples were grouped into three clusters, one of which was further classified into two clusters in our third-step analysis. In conclusion, we detected a hierarchical structure among Varied Tits breeding on the Izu Islands and inferred that ancestors of the owstoni group colonized from the mainland more recently than those of the namiyei group.