Designing fishing policies without knowledge of past levels of target species abundance is a dangerous omission for fisheries management. However, as fisheries monitoring started long after exploitation of many species began, this is a difficult issue to address. Here we show how the ‘shifting baseline’ syndrome can affect the stock assessment of a vulnerable species by masking real population trends and thereby put marine animals at serious risk. Current fishery data suggest that landings of the large Gulf grouper (Mycteroperca jordani, Serranidae) are increasing in the Gulf of California. However, reviews of historical evidence, naturalists’ observations and a systematic documentation of fishers’ perceptions of trends in the abundance of this species indicate that it has dramatically declined. The heyday for the Gulf grouper fishery occurred prior to the 1970s, after which abundance dropped rapidly, probably falling to a few percent of former numbers. This decline happened long before fishery statistics were formally developed. We use the case of the Gulf grouper to illustrate how other vulnerable tropical and semi-tropical fish and shellfish species around the world may be facing the same fate as the Gulf grouper. In accordance with other recent studies, we recommend using historical tools as part of a broad data-gathering approach to assess the conservation status of marine species that are vulnerable to over-exploitation.