The end-Permian mass extinction, the most severe biocrisis in Earth history, has been attributed to major flood basalt volcanism, but direct evidence of volcanic effects on contemporaneous marine biotas is scarce. In this study, we examined the relationship of two components of the microplankton community (acritarchs and radiolarians) to volcanic ash deposits in two deepwater sections from South China (Shangsi and Xinmin). In these sections, each eruptive event was recorded as a volcanic couplet consisting of a pale, 0.1 to 3.0-cm-thick bentonite (altered volcanic ash) overlain by a dark, 0.1- to 1.0-cm-thick, organic-rich mudstone layer. Acritarchs were found in peak abundance in the mudstone overlying each ash layer but were otherwise present only in low concentrations in the background sediment. In contrast, radiolarians were rare in the volcanic couplets but frequently abundant in the background intervals. The thickest volcanic ash layers in both sections are found immediately below and above the latest Permian mass extinction (LPME) horizon. At this level, radiolarians underwent a major regional extinction but acritarchs reached their peak abundance, confirming their role as a disaster taxon. Above the LPME, long-spined and small spherical acritarchs declined more rapidly than short-spined forms. The preference of the short-spined acritarchs for neritic inner-shelf facies may indicate that such areas served as biotic refugia during intervals of extreme environmental stress. We infer that volcanic eruptions during the Permian–Triassic transition had both positive effects (e.g., increased nutrient supply) and negative effects (e.g., metal toxicity, lowered seawater pH, increased turbidity) on marine microplankton communities, the importance of which varied both spatially and temporally.