A widespread marine microbialite and underlying truncation surface occur in Permian–Triassic sections of South China. We interpret the microbialite to have formed as a shallow, open-marine benthic framework stimulated by high seawater CaCO₃ saturation. The widespread distribution across platform interiors and lack of asymmetry or thickening toward platform margins is incompatible with an alternative hypothesis, that microbialite deposition was stimulated by upwelling anoxic, alkaline waters. The truncation surface beneath the microbialite is irregular with overhangs and small caverns extending up to 30 cm beneath the surface indicating a dissolutional origin. Petrographic observations refute the interpretation that strata immediately beneath the surface contain pendant cements, meniscus cements, and vadose silt. Measurements of the anisopachous fibrous cements show that thickened areas have random, not downward orientations. Pores retain the pointed geometry consistent with isopachous cement. Carbon and oxygen isotope measurements, from immediately beneath the surface, do not show a negative shift as would be expected with subaerial exposure. Also incompatible with a subaerial origin is the occurrence of only one truncation surface within a subtidal succession ~ 50 m thick below the surface and the limited vertical penetration of dissolution. The surface closely resembles a hardground containing a micritized alteration zone with stromatolites encrusted on the surface. We interpret the surface to have formed by submarine dissolution driven by a pulse of ocean acidification associated with Siberian Traps eruptions and the end-Permian extinction. After a hiatus of ~ 30–100 kyr, seafloor dissolution would have brought seawater back to saturation coupled with increased delivery of calcium to the oceans as the result of elevated continental weathering and caused a rebound in carbonate saturation and precipitation of microbialites.