In times of increased human interventions, knowledge on animal breeding-site fidelity is crucial for the conservation of important reproduction areas vital to the resilience of populations. In particular, in the marine environment, dependency of ocean-going fish on specific coastal locations are rarely implemented in spatial planning. However, when essential nursery habitats are threatened, the resilience of fish populations is jeopardized. For technical reasons, former studies on Atlantic herring could not specify if fish, returning to spawning grounds, returned to sites of their own natal origin. Combining otolith microchemistry with genetics, we show that Atlantic herring perform natal homing with rates between 56 and 73%. The implicit number of strays adopted along migration maintain the gene flow between subpopulations, supporting the hypothesized “metapopulation” concept. With respect to increasing anthropogenic impacts, this study demonstrates the need for a goal-oriented coastal zone management to ensure productive ecosystems and a sustainable fishery in the future.