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Most edible fish species have been fished for centuries or millennia, leaving little record or understanding of their population responses prior to human impact and thus no baseline for population conservation. Here, we reconstruct the population dynamics of Atlantic cod, one of the world’s most harvested fish species, from the pristine state during the Viking era through more than 1100 years of fishing. Analysis of cod otoliths recovered during archaeological excavations of Icelandic fish processing sites revealed that cod in the 10th to 12th centuries were 25% larger and up to 300% older than modern, despite slower density-dependent growth rates attributed to the sixfold increase in abundance. Fishing mortality came to dominate a time-invariant natural mortality rate and other population characteristics after the 14th century, with minimal evidence of environmental effects at the century scale. Despite the absence of catch records and surveys, biological reference points based on pristine fish populations are now possible where otolith collections are available.