Massive occurrences of microbialites near the Permian-Triassic boundary have been interpreted as being due to benthic microbial proliferation in unusual marine conditions after the end-Permian mass extinction. Here, we present large populations of Polybessurus-like microfossils in the microbialites of the South China Craton to reveal their morphological structures, growth patterns, and ecological implications. These distinctive microfossils are composed of layered stalks and spherical endpoints. The spheroids, 20-40 mu m in diameter, comprising external thin micritic walls and internal sparry parts, are interpreted as coccoid cyanobacteria. The stalks consist of multiple "stacked-cup" micritic envelopes consisting of micron-sized magnesian calcite/dolomite grains and are catalogued as calcified remains of coccoid cyanobacterial extracellular polymeric substances (EPS). Early microbially mediated calcification of EPS increased the preservation potential of microfossils. The microfossils stand upright as coccoid unicells supported by the highly unidirectional secretion of EPS, revealing their benthic behaviours. The successively secreted EPS lift the cells away from the substrate, expanding their ecological niches to gain more sunlight for photosynthesis in the barren marine floor. The distinctive Polybessurus-like microfossils can be viewed both in laminae of stromatolites and in spotted/digitate clots of thrombolites, suggesting their critical roles in microbe-dominated reefs in the aftermath of the end-Permian mass extinction. The morphological features and growth patterns of the Polybessurus-like fossils resemble their Proterozoic counterpart-Polybessurus bipartitus Fairchild ex Green et al. (1987). The widespread Polybessurus-like fossils in the Permian-Triassic boundary microbialites of the South China Craton suggest pervasive retrogressive ecosystems on carbonate platforms after the largest extinction event during the Earth's history.