Stromatolites are commonly viewed as sedimentary proxies for microbial communities. In consequence, secular variation in stromatolite form has been attributed to evolutionary change in mat organisms and/or their interactions with global environments. This interpretation requires that one be able to identify features of stromatolite macrostructure or microstructure that are under direct biological influence and use them to document the sedimentological or petrological consequences of microbial evolution. Well-preserved stromatolites in Proterozoic carbonates of the Siberian Platform contain two distinctive types of microstructure that enable us to address such issues. Preserved microstructures in Baicalia lacera and Tungussia confusa from lower Neoproterozoic (lower Upper Riphean) platform carbonates of several widely separated regions clearly reflect the biology of underlying mat communities; mm-scale laminae of densely interwoven calcified filaments alternate with filament-poor microspar. Comparable carbonate microstructures are known from a number of other Neoproterozoic stromatolites, but are as yet unreported from older successions. Filamentous cyanobacteria formed mats throughout the Proterozoic Eon; thus, the temporal distribution of this microstructure appears principally to reflect secular and environmental variations in carbonate cementation and diagenesis. Omachtenia omachtensis is the characteristic stromatolite of Mesoproterozoic (Lower and, occasionally, Middle Riphean) successions of the Siberian Platform and elsewhere. Its distinctive microstructure consists of mechanically deposited event laminae separated by thin organic films that served as nucleation sites for micritic and, less commonly, fibro-radiate carbonate precipitates. Microbial mats may have stabilized sediments between events, but there is little evidence that mats played an active role in the trapping and binding or precipitation of laminae. Thus, physico-chemical factors must also be responsible for the distribution of these stromatolites in time and space. Analysis of these two microstructures suggests that, in general, secular trends in stromatolite microstructure may encrypt important information about environmental change through the Proterozoic Eon. Microbial evolution may also play a role in determining the stratigraphic distributions of particular Proterozoic stromatolites, but this remains to be demonstrated. Evolution may be most important in driving the progressive environmental restriction of stromatolite-forming microbial communities through time.