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Background Conserving migratory birds is challenging due to their reliance on multiple distant sites at different stages of their annual life cycle. The concept of “flyway”, which refers to all areas covered by the breeding, nonbreeding, and migrating of birds, provides a framework for international cooperation for conservation. In the same flyway, however, the migratory activities of the same species can differ substantially between seasons and populations. Clarifying the seasonal and population differences in migration is helpful for understanding migration ecology and for identifying conservation gaps. Methods Using satellite-tracking we tracked the migration of Whimbrels (Numenius phaeopus variegatus) from nonbreeding sites at Moreton Bay (MB) and Roebuck Bay (RB) in Australia in the East Asian–Australasian Flyway. Mantel tests were used to analyze the strength of migration connectivity between the nonbreeding and breeding sites of MB and RB populations. Welch’s t test was used to compare the migration activities between the two populations and between northward and southward migration. Results During northward migration, migration distance and duration were longer for the MB population than for the RB population. The distance and duration of the first leg flight during northward migration were longer for the MB population than for the RB population, suggesting that MB individuals deposited more fuel before departing from nonbreeding sites to support their longer nonstop flight. The RB population exhibited weaker migration connectivity (breeding sites dispersing over a range of 60 longitudes) than the MB population (breeding sites concentrating in a range of 5 longitudes in Far Eastern Russia). Compared with MB population, RB population was more dependent on the stopover sites in the Yellow Sea and the coastal regions in China, where tidal habitat has suffered dramatic loss. However, RB population increased while MB population decreased over the past decades, suggesting that loss of tidal habitat at stopover sites had less impact on the Whimbrel populations, which can use diverse habitat types. Different trends between the populations might be due to the different degrees of hunting pressure in their breeding grounds. Conclusions This study highlights that conservation measures can be improved by understanding the full annual life cycle of movements of multiple populations of Whimbrels and probably other migratory birds.