The reefs of the middle-late Cambrian (Cambrian Epoch 3-Furongian) have long been simply considered as microbialites that flourished in the aftermath of the archaeocyath extinction. Thorough review of the reefs in these periods shows, however, that the Cambrian Epoch 3 and the Furongian actually yield different types of reefs. The Cambrian Epoch 3 reefs are dominated by thrombolites and dendrolites, largely constructed by the calcified microbes Epiphyton and Renalcis. On the other hand, the Furongian reefs consist mainly of maze-like maceriate reefs and columnar stromatolites. The maceriate reefs most likely formed by siliceous sponges and calcified microbes including Girvanella and Tarthinia, whereas the columnar stromatolites were mainly constructed by Girvanella, Tarthinia, and minor siliceous sponges. Other microbial reefs (e.g., non-columnar stromatolites) persisted during the Cambrian Epoch 3 and the Furongian, mainly as small patch reefs or reefal crusts. Lithistid sponge-microbial reefs initially formed in the Cambrian Epoch 3 and occurred throughout the Furongian, but occupied only a minor portion during these periods.Several geological events occurred across the boundary between the Cambrian Epoch 3 and the Furongian, including positive carbon and sulfur isotope excursions, a eustatic sea-level drop, major faunal turnover of trilobites, and diversification of new organisms. The coincidence of these events and the transition in reefal fabrics suggest that reef ecosystems were significantly influenced by at least some of these events. Among the events, it is likely that sea-level change would have affected reefs, although further studies are required in order to test whether and how the other events influenced the reef transition. Epiphyton and Renalcis (and thrombolites and dendrolites formed by them) declined greatly most likely due to sea-level fall and thus decreased in shallow marine habitat at the end of Cambrian Epoch 3. The Cambrian Epoch 3 thrombolites and dendrolites were gradually replaced by a sponge-microbial association of the maze-like, maceriate reefs and the columnar stromatolites in the Furongian, coincident with a sea-level rise.