One of the most severe extinctions of complex marine life in Earth’s history occurred at the end of the Triassic Period (~200 million years ago). The end-Triassic extinction was initiated by large igneous province volcanism and has tentatively been linked to the spread of anoxic conditions. However, the global-scale pattern of anoxic conditions across the end-Triassic event is not well constrained. Here we use the sedimentary enrichment and isotopic composition of the redox-sensitive element molybdenum to reconstruct global–local marine redox conditions through the extinction interval. Peak δ98Mo values indicate that the global distribution of sulfidic marine conditions was similar to the modern ocean during the extinction interval. Meanwhile, Tethyan shelf sediments record pulsed, positive δ98Mo excursions indicative of locally oxygen-poor, sulfidic conditions. We suggest that pulses of severe marine de-oxygenation were largely restricted to marginal marine environments during the latest Triassic and played a substantial role in shallow marine extinction phases at that time. Importantly, these results show that global marine biodiversity, and possibly ecosystem stability, were vulnerable to geographically localised anoxic conditions. Expanding present-day marine anoxia in response to anthropogenic marine nutrient supply and climate forcing may therefore have significant consequences for global biodiversity and wider ecosystem stability.