Diverse stromatolitic structures are recognized in the Meso-Neoproterozoic basins in southern East Siberia: simple (bioherms and biostromes), individual, barrier, shore reefs and reef-like structures, and large reef-like banks. These data and results of macro- and microscopic studies of stromatolites point to the leading role of microbial communities in the production of primary carbonate material. Most of the carbonate mud was supplied to the deep-water shelf zones, slopes, and plains of the Meso-Neoproterozoic East Siberian basins from shallow-water shelves. Analysis of the materials from almost all Precambrian carbonate complexes shows that the microbial communities have played the leading role in the generation of carbonate material since the Late Mesoarchean. Both the shallow- and deep-water Precambrian carbonate sedimentary systems have much in common with the Phanerozoic ones. Their diversity and development are controlled by a number of factors, which exert different effects in geodynamically different basins, and the carbonate systems of different ranks are fine indicators of various events in the basin evolution, from the low-amplitude eustatic fluctuations of the sea level to the global epochs of flooding and highstand of supercontinents. The absence of lime-producing organisms in the Precambrian determined the similar composition of carbonate rocks and sometimes the indistinct structure-morphologic differentiation of the Precambrian organogenic structures. The evolution of reef systems in the Precambrian was determined first of all by the evolution of the lithosphere, which periodically led to the formation and cessation of development of basins favorable for the mass evolution of microbial communities, and by the structural complication of microbial communities producing stromatolites. The epochs of stromatolite formation reduction and destruction of sea basins correlate well with the global epochs of the formation and highstand of supercontinents.