This paper reviews the current progress and problems in the study of microbialites and microbial carbonates. Microbialites and microbial carbonates, formed during growth of microbes by their calcification and binding of detrital sediment, have recently become one of the most popular geological topics. They occur throughout the entire geological history, and bear important theoretical and economic significances due to their complex structures and formative processes. Microbialites are in place benthic microbial buildups, whereas microbial carbonates can be classified into two categories: stabilized microbial carbonates (i.e., carbonate microbialites, such as stromatolites and thrombolites) and mobilized microbial carbonates (i.e., microbial carbonate grains, such as oncoids and microbial lumps). Various texture, structures, and morphologies of microbialites and microbial carbonates hamper the systematic description and classification. Moreover, complex calcification pathways and diagenetic modifications further obscure the origin of some microbialites and microbial carbonates. Recent findings of abundant sponge spicules in previously identified “microbialites” challenge the traditional views about the origins of these “microbialites” and their implications to reef evolution. Microbialites and microbial carbonates did not always flourish in the aftermath of extinction events, which, together with other evidences, suggests that they are affected not only by metazoans but also by other geological factors. Their growth, development, and demise are also closely related to sea-level changes, due to their dependence on water depth, clarity, nutrient, and sunlight. Detailed studies on microbialites and microbial carbonates throughout geological history would certainly help understand causes and effects of major geological events as well as the co-evolution of life and environment.