Following the Frasnian–Famennian mass extinction, which eliminated most skeletal reef-building fauna, the early Famennian reefs of the Canning Basin were constructed primarily by reef-framework microbial communities. In the Napier and Oscar Ranges, the Famennian reef complexes had high-energy, reef-flat depositional environments on a reef-rimmed platform that transitioned into low-energy, deep-water reefs growing in excess of 50 m below sea level. High-energy, reef-flat depositional environments contain doming fenestral stromatolites that grade into porous thrombolites and are associated with coarse-grained sandstones and grainstones. The reef-margin subfacies contains mounds of microdigitate thrombolites, which are more delicate than the reef-flat thrombolites and locally contain abundant red algae, Girvanella, renalcids and sediment-filled tubes. Within the thrombolites, the red algae are in upright growth positions, suggesting that the thrombolites are largely composed of carbonate that precipitated in situ. Reefal-slope environments are dominated by Wetheredella and Rothpletzella with locally abundant Girvanella, renalcids and Uralinella. In reefal-slope strata, delicate fans and microdigitate stromatolites of Wetheredella and Rothpletzella are often oriented horizontal or diagonal to bedding and are interpreted as syndepositionally toppled over. Most mesoscale microbial community structures contain several species of microbial fossils, and no single microbial species appears to have controlled the morphology of the community structure. Therefore, the depositional environment must have determined the distribution and morphology of the stromatolites, thrombolites and other microbial community structures. The adaptability of microbial communities to various reef environments allowed them to fill ecological niches opportunistically after the Frasnian–Famennian mass extinction.