After the latest Permian mass extinction event, microbial mats filled the ecological niche previously occupied by metazoan reefs, resulting in widespread microbialites. This study focuses on the lipid biomarker (molecular fossil) and invertebrate fossil records from Neotethyan platform margin sections to understand microbial-metazoan bioherm formation. Here, we find that early Griesbachian thrombolitic and stromatolitic microbialites from Çürük Dag (Turkey) and Kuh e Surmeh (Iran) contain abundant lipid biomarkers, representing input from cyanobacteria, anoxygenic phototrophic bacteria, sulfate-reducing bacteria, and halophilic archaea. The biomarker inventory suggests that the microbialites were constructed by cyanobacteria-dominated microbial mats. Biomarkers of halophilic archaea are interpreted to reflect input from the water column, suggesting that the Neotethys experienced at least episodically hypersaline conditions. We also demonstrate that bacteria, possible keratose sponges (up to 50% of the carbonate is represented by the possible sponges), and microconchids lived synergistically to form microbial-metazoan bioherms in the immediate aftermath of the extinction along the western margin of the Neotethys. Abundant fossils of oxygen-dependent invertebrates (i.e. microconchids, bivalves, gastropods, brachiopods, and ostracods) and foraminifers were also found within these bioherms. The presence of invertebrates in conjunction with abundant molecular fossils of cyanobacteria indicates an oxygenated water column. Even though the presence of the biomarker isorenieratane in microbialites may considered as evidence for euxinic conditions in the water column, its absence in the background sediments rather points to a source organism belonging to the mat community. The new finding of bioherms built in part by metazoans suggests that reef ecosystems underwent a major turnover across the extinction event, and shortens the ‘metazoan reef gap’ to just the uppermost Changhsingian. During the Early Triassic, therefore, reefal ecosystems were able to recover in oxygenated settings since the earliest Griesbachian, albeit in an impoverished state.