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1. Anthropogenic activities have resulted in declines in many marine turtle populations. Their complex life cycle (e.g. female philopatry, hatchling migration, adult movements between breeding and foraging areas) makes it difficult to fully understand some of the biological implications of human impacts on their populations, but genetic tools can play a major role in understanding population dynamics and thus improve conservation and management strategies. 2. Using the mitochondrial DNA control region, this study examines the composition, population structure, and connectivity between rookeries and foraging aggregations, in addition to their relationship with Atlantic rookeries and foraging areas of the hawksbill turtle in the Yucatan Peninsula. 3. Haplotype composition of rookeries showed EiA22, EiA39, and EiA41 as endemic haplotypes and revealed a segregation between the Gulf of Mexico and the Yucatan and Quintana Roo rookeries, defining two management units. Foraging aggregations present 15 haplotypes, some common for Atlantic and others for Mexican rookeries. Considering the Gulf of Mexico versus the Mexican Caribbean, significant population genetic structure was revealed, inferring a differential recruitment of hawksbill turtles. 4. Rookery‐centric mixed‐stock analysis reveals a high contribution of Mexican turtles to local foraging aggregations, principally in the Gulf of Mexico. Foraging‐groundcentric mixed‐stock analysis showed that the Gulf of Mexico foraging aggregation is predominantly composed of individuals from local rookeries, whereas Mexican Caribbean foraging groups have a mixed composition with individuals from Barbados, Brazil, and Puerto Rico rookeries. The connectivity between rookeries and foraging aggregations suggests that the ocean currents and swimming behaviour influence the distribution of hawksbill turtles. 5. Our results highlighted the importance in identifying management units in nesting and foraging areas to develop monitoring and management programmes at appropriate geographic scales. In addition, understanding turtle habitat connectivity will allow for prioritized conservation actions considering particular threats, emphasizing the need for both national and international collaboration for conservation of this endangered species. Inglés