Description: Highlights: • We combine high-resolution ocean models with population genetics • Variation in wind-driven ocean currents mediates the collapse of A. anguilla • Female eels are philopatric within the Sargasso Sea, while males maintain gene flow • We present first evidence of the role of ocean currents in shaping species’ evolution Summary: Worldwide, exploited marine fish stocks are under threat of collapse [1]. Although the drivers behind such collapses are diverse, it is becoming evident that failure to consider evolutionary processes in fisheries management can have drastic consequences on a species’ long-term viability [2]. The European eel (Anguilla anguilla; Linnaeus, 1758) is no exception: not only does the steep decline in recruitment observed in the 1980s [ 3 and 4] remain largely unexplained, the punctual detection of genetic structure also raises questions regarding the existence of a single panmictic population [ 5, 6 and 7]. With its extended Transatlantic dispersal, pinpointing the role of ocean dynamics is crucial to understand both the population structure and the widespread decline of this species. Hence, we combined dispersal simulations using a half century of high-resolution ocean model data with population genetics tools. We show that regional atmospherically driven ocean current variations in the Sargasso Sea were the major driver of the onset of the sharp decline in eel recruitment in the beginning of the 1980s. The simulations combined with genotyping of natural coastal eel populations furthermore suggest that unexpected evidence of coastal genetic differentiation is consistent with cryptic female philopatric behavior within the Sargasso Sea. Such results demonstrate the key constraint of the variable oceanic environment on the European eel population.