Dunlin (Calidris alpina) is a polymorphic species with a complex of subspecies. A migration stopover site on the intertidal mudflats of Jiangsu Province, China, has a pivotal role in the migratory connectivity of dunlin along the East Asian–Australasian Flyway (EAAF). However, to date, the dunlin subspecies that visit the coast of China during migration remains uncertain. To determine the subspecies, an integrated approach based on mitochondrial DNA, ring recoveries, and morphological traits was used to analyze dunlins sampled at the Jiangsu stopover site. Alaskan and Beringian lineages were the two dominant lineages that migrated through Jiangsu, and the number of dunlins from the Alaskan lineage greatly exceeded that from other lineages. According to genetic analysis, the proportion of identified lineages was greater than 70%. At least four subspecies were detected in eastern Jiangsu Province, including C. a. actites, C. a. kistchinski, C. a. sakhalina, and C. a. arcticola. There were significant differences in morphological characters between years, suggesting that proportions of subspecies at the stopover varied over time and that different subspecies adopted different migratory strategies and timings. The findings of this study highlight the need to further consider how subspecies contribute to the composition of populations and migratory connectivity of dunlin.