Human impact often leads to the decline or loss of native biodiversity. The European oyster (Ostrea edulis L.) is a prominent example for such decline. Abundant and cheap seafood in the past, is the oyster today a sought after delicacy. This change is a consequence of the sharp decline of wild oyster populations in the 20th century. In the North Sea, the European oyster vanished altogether in the 1950s, and has not been able to reclaim its original habitat. What prevents a successful recolonization? Was the original population locally-adapted to the specific North Sea conditions, and oysters from other regions are unable to survive those conditions? Answering these questions requires to travel back in time to investigate a now-extinct population. The Zoological Museum holds the key for such time travel: an extensive collection of oyster shell from all over Europe – including the now extinct North Sea population – collected by Karl-August Möbius around 1870. Using museum genomics, we sequenced over 100 oysters from across Europe that were collected in the 1870s. The North Sea populations show a high degree of unique diversity, which could clearly be responsible for their local extinction.