The end-Triassic mass extinction coincided with the eruption of the Central Atlantic Magmatic Province, a large igneous province responsible for the massive atmospheric input of potentially climate-altering volatile compounds that is associated with a sharp rise in atmospheric CO2. The extinction mechanism is debated, but both short-term cooling (~10s of years) related to sulfur aerosols and longer-term warming (10,000 yrs) related to CO2 emissions—essentially opposite hypotheses—are suggested triggers. Until now, no temperature records spanning this crucial interval were available to provide a baseline or to differentiate between hypothesized mechanisms. Here, we use clumped-isotope paleothermometry of shallow marine microbialites coupled with climate modeling to reconstruct ocean temperature at the extinction horizon. We find mild to warm ocean temperatures during the extinction event and evidence for repeated temperature swings of ~16 °C, which we interpret as a signature of strong seasonality. These results constitute the oldest non-biomineralized marine seasonal temperature record. We resolve no apparent evidence for short-term cooling or initial warming across the 1-80kyr of the extinction event our record captures, implying that the initial onset of the biodiversity crisis may necessitate another mechanism.