Upwelling of cold, nutrient-rich water from the oxygen minimum zone (OMZ) off Peru sustains the world’shighest production of forage fish, mostly composed of anchovy (Engraulis ringens). However, the potentialimpacts of climate change on upwelling dynamics and thus fish productivity in the near future areuncertain. Here, we reconstruct past changes in fish populations during the last 25,000 years to unraveltheir response to changes in OMZ intensity and productivity. We quantified and identified fish scales andbones deposited in laminated sediments from Pisco (Peru) with an average sampling resolution of 20.4years (±7.1). The records span the Last Glacial Maximum to the recent Holocene and thus encompass avariety of combinations of productivity, oxygen, and global temperature. Our results reveal thatproductivity appears to be the main factor controlling small pelagic fish abundance, while sub-surfaceoxygenation affects mainly anchovy and likely sardine populations. Lower productivity and higher oxygenconcentrations during the glacial resulted in lower total fish productivity, whereas higher productivity anda stronger OMZ in some time intervals during the Holocene resulted in higher fish abundances. A varietyof different conditions between these two oceanographic end members indicate preferred environmentalconditions for a variety of small pelagic fishes. There is no evidence in our record for an out of phaserelationship between anchovy and sardine at the timescales examined in the present study. Anchovy havebeen the predominant small pelagic fish throughout the record, at least over centennial to millennialtimescales. Its abundance reached a maximum during the Current Warm Period, an era characterized byhigh productivity and intense OMZ conditions. Thus, industrial fisheries developed during a period ofexceptional productivity in relation to that of the last 25 kyr. The records reveal that dramatic decreasesin pelagic fish abundances have occurred in response to past large-scale climate changes than thoseobserved in the instrumental period, which suggests that future climate change may result in substantialchanges in ecosystem structure.