During the Late Devonian mass extinction, Frasnian coral-stromatoporoid reefs were replaced by Famennian microbialites, with the Upper Kellwasser event at the Frasnian-Famennian boundary marking the primary extinction phase. However, its impact on reef ecosystems is not well-understood, especially in South China, and roles of microbes are controversial as most studies focus on specific intervals, i.e. Frasnian or Famennian. This study provides facies analysis of a continuous Frasnian-Famennian shallow-water section at Quanzhou, Guiling in South China, offering insights into evolution of a Late Devonian reef ecosystem. At the Quanzhou section, late Frasnian metazoan-microbial reefs contain abundant microbial components, displaying a gradual decline of coral-stromatoporoid toward the Frasnian-Famennian boundary. The Upper Kellwasser event bed was constrained by conodonts, macrofossils and carbon isotope chemostratigraphy, corresponding to the onset of a positive delta 13C excursion (+3 parts per thousand) as well as loss of skeletal builders. Its event bed is a 1.5m-thick thrombolitic stromatolite unit which may have formed by a local boom of microbes. Early Famennian wacke-packstones contain abundant microbial aggregated grains. Intensive bioturbation indicated by clotted texture and minor bioclasts suggests infaunal activities were not suppressed. Notably, microbes played a significant role in both Frasnian and Famennian reef construction and carbonate deposits, with the Upper Kellwasser event potentially triggering a disaster microbe bloom at the Quanzhou section. Therefore, the role of microbes before, during, and after an extinction may be more complex than previously recognized.