Global fossil data show that profound biodiversity loss preceded the final catastrophe that killed nearly 90% marine species on a global scale at the end of the Permian. Many hypotheses have been proposed to explain this extinction and yet still remain greatly debated. Here, we report analyses of all four sulphur isotopes ((32)S, (33)S, (34)S and (36)S) for pyrites in sedimentary rocks from the Meishan section in South China. We observe a sulphur isotope signal (negative δ(34)S with negative Δ(33)S) that may have resulted from limitation of sulphate supply, which may be linked to a near shutdown of bioturbation during shoaling of anoxic water. These results indicate that episodic shoaling of anoxic water may have contributed to the profound biodiversity crisis before the final catastrophe. Our data suggest a prolonged deterioration of oceanic environments during the Late Permian mass extinction.