Widespread but episodic deposition of cyanobacterial mats occurred during the 5 m.y. Permo-Triassic biotic crisis, providing a critical record to decipher the long-term stressful environmental conditions and thus a linkage with the killer. Here we document the timing and duration of these blooms, indicated by lipid biomarkers and microbialites, throughout South China and compare them to the timing of volcanic activity. The initial cyanobacterial bloom has the longest duration and is associated with a prominent Eu anomaly in southwestern China, where the most intensive volcanism has been proposed to occur, suggesting a causal relationship. Subsequent cyanobacterial blooms in the Early Triassic are associated with known volcanic events in South China and also with the most voluminous Siberian flood basalts, and with the largest negative carbon isotope excursions. Thus, it appears that volcanic activity has had a significant impact on microbial development in South China. South China volcanism around the Permian-Triassic boundary (PTB) could have played a much larger role in biotic changes of both bacterial and calcified faunal ecosystems than previously thought. The well-known Siberian volcanism is proposed herein, on the basis of the current compilation of dating data, to protract the Early Triassic faunal recovery rather than to cause the end-Permian extinction.