Natural selection could not fully explain the diversity of avian migratory routes in the previous studies, possibly because historical contingency, another important evolutionary driver, has not been considered. In this study, owing to the benefits of an island system as the natural laboratory, I investigated the relative contribution of historical contingency in the evolution of migratory routes of two nocturnal migratory passerines (Lanius cristatus and Saxicola stejengeri) in the Japanese Archipelago. Empirical migratory routes of the two species were tracked by light-level geolocators, and they were compared to simulated migratory paths under two different scenarios. One scenario considered only natural selection (adaptation scenario), whereas the other considered both natural selection and historical contingency (contingency scenario). In the contingency scenario, migratory routes were assumed to be constrained by possible historical colonisation source areas to Japanese islands. Overall, results showed that the contingency scenario better reflected the empirical routes than the adaptation scenario. Meanwhile, the pattern was reversed in the spring migratory routes of Saxicola stejnegeri, which can be explained by stronger selective pressures in spring than in autumn. These results suggest that historical contingency is an important evolutionary driver alongside natural selection in shaping the present migratory routes.