The evolution of complex life over the past 600 million years was disrupted by at least five mass extinctions, one of which occurred at the close of the Triassic period. The end-Triassic extinction corresponds to a period of high atmospheric-CO2 concentrations caused by massive volcanism and biomass burning; most extinction scenarios invoke the resulting environmental perturbations in accounting for the loss of marine and terrestrial biodiversity. Here we reconstruct changes in Tethyan shallow marine ecosystems and ocean redox chemistry from earliest Jurassic (Hettangian)-aged black shales from Germany and Luxemburg. The shales contain increased concentrations of the biomarker isorenieratane, a fossilized pigment from green sulphur bacteria. The abundance of green sulphur bacteria suggests that the photic zone underwent prolonged periods of high concentrations of hydrogen sulphide. This interval is also marked by the proliferation of green algae, an indicator of anoxia. We conclude that the redox changes in the entire water column reflect sluggish circulation in marginal regions of the Tethys Ocean. We suggest that the resultant repeated poisoning of shallow epicontinental seas—hotspots of Mesozoic biodiversity—with hydrogen sulphide may have slowed the recovery of marine ecosystems during the Early Jurassic.