Marine heatwaves are globally occurring events that can negatively impact fisheries, but their impacts on small-scale operations remain understudied. We investigate the historical and future impacts of marine heatwaves on small-scale fisheries operating along a biogeographic transition zone in the Baja California Peninsula, Mexico. We estimate the impacts of the most intense marine heatwave regime on record on fisheries production of 43 economic units operating in a system of 55 Territorial Use-Rights for Fisheries. During this regime, aggregate landings in the lobster, sea urchin, and sea cucumber fisheries decreased between 15 and 58%. Most operations (56%) presented large reductions in landings, whose losses more than outweigh the small increase detected for the other 44%. Notably, impacts were larger for fisheries operating near an equatorward biogeographic break, and for operations in areas of high historical environmental variation and low historical variation in fisheries production. Climate models predict an increase in the frequency and intensity of exposure to marine heatwaves for all fisheries, but the change in frequency and intensity will be greater for those in the north. In the face of extreme environmental shocks such as marine heatwaves, small-scale fisheries operating near biogeographic transition zones are among the most vulnerable.