Microbes, as essential components of any ecosystem for their metabolic capabilities of driving energy and matter cycles, must have been omnipresent in the earliest metazoan-dominated marine ecosystem that was initially established during the Ediacaran-Cambrian transition. However, contemporaneous microbial fossils and their ecological roles are rarely known. Here we report an exquisitely preserved microbial fossil assemblage from the ∼535 million years old phosphorite of South China. Ten types of filamentous and spherical fossils have been identified and most are comparable to modern fungi, cyanobacteria, and microalgae at a cellular level. Particularly, mold- and yeast-like morphotypes that are interpreted as fungi provide potential fossil evidence for exploring the early evolution of fungi. This microbial assemblage including fungal and cyanobacterial analogues built symbiotic mats composed of decomposers and producers that were ecologically indispensable for early metazoans. A rapid phosphatization followed by silica-cementation is responsible for the high fidelity of fossil preservation, and hence is an ideal taphonomic window to explore the microbial world in geological past.