Understanding changes in bacterial-algal communities is vital for unraveling climato-environmental factors linking ultimate triggers (e.g., volcanic, bioevolutionary, and tectonic events) and proximate killers (e.g., temperature and redox) in biocrises. However, the dynamics of marine community evolution during the two main extinction pulses of the Late Ordovician Mass Extinction (LOME), the first at the Katian-Hirnantian boundary and the second in the late Hirnantian, remain poorly investigated. Here, using multiple biomarkers (i.e., steranes, hopanes, moretanes, gammacerane, and n-alkanes), we document changes in red-algal/green-algal and bacteria/eukaryote ratios, along with the response of certain microbes sensitive to oceanic stratification and soil erosion through the Ordovician-Silurian transition. The distributions of these biomarkers reveal increased primary productivity and decreased continental weathering and oceanic stratification during the LOME-1, with the opposite trend during the LOME-2. Correlating these finding with global climato-environmental records, we infer that elevated productivity stimulated local expansion of oceanic anoxia and contributed to the culmination of a long-term cooling trend during the LOME-1, whereas rising temperatures and sea levels promoted intensified oceanic stratification and regionally anoxic conditions during the LOME-2. The results of the present study provide significant new biological constraints on the causation of the LOME.