The genetic structure of Streaked Shearwater Calonectris leucomelas, a seabird breeding on islands around Japan, was investigated using nuclear microsatellite markers at four breeding colonies located in three geographically distinct areas (Pacific Ocean, Sea of Japan, and Seto Inland Sea). To investigate independently natal and breeding dispersal patterns, we analyzed records of recoveries of birds banded around Japan over a 30-year period from 1971 to 2020. The genetic marker analysis showed little differentiation among the breeding sites and a lack of population structure. In contrast, banding data presented few examples of natal and breeding dispersal and a much greater number of natal/breeding philopatry cases. Although further research is needed to understand the discrepancy between the genetic properties and recapture patterns of banded birds, some possible reasons are suggested: actual dispersal events may not have been fully detected by the banding research, thus, underestimating dispersal frequency; rare dispersal events may have functioned to reduce the genetic structure; and/or breeding colonies of this species might have been established recently, thus genetic markers may not be indicative of current dispersal patterns. In conclusion, our results indicate ongoing gene flow and/or strong historical association in this species.