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The COVID-19 pandemic is expected to have significant consequences for wildlife populations and conservation efforts, particularly in driving an increase in illegal extraction at the local and regional level. Here, we report a shift in illegal catch by both commercial and recreational fishing vessels inside and outside the Alcatrazes Archipelago marine protected area, a biodiversity hotspot in the southwest Atlantic Ocean, for the three years before and two years during the pandemic. We witnessed an increase in both the total illegal catch and numbers of species caught since the pandemic, particularly by amateur fishers. Both types of vessels targeted larger, more valuable apex predators during the pandemic, including many threatened and endangered species. Based on a functional trait analysis, removal of these species is likely to have significant ecosystem sequences into the future. Our study provides new evidence that the pandemic can significantly reduce the effectiveness of marine conservation.