Cryptic microbialites in the Heron Reef framework occur as crusts of fingerlike microcolumns or branching dendrolites, rarely more than 1 cm long. Microstructure of the most recently growing microbialite surfaces consists of coalesced, <0.5 µm, rounded Mg-calcite crystallites forming smooth, thin crusts that are interpreted as calcified mucus within the basal layer of a biofilm. The crystallites become larger and more euhedral from the tip toward the base of the microcolumn. A similar progression occurs from the surface to the interior of the microbialites, yielding, at the bases of microcolumns, >3 µm scalenohedra that are indistinguishable from previously described Mg-calcite “abiotic” cement. The transformation from submicrometer, anhedral crystallites to >3 µm scalenohedra is inferred to have occurred only during active microbialite accretion beneath a biofilm. This syngenetic change from primary, biologically induced microstructures to microstructures that are indistinguishable from abiotic cement has important implications for the recognition and interpretation of early marine microcrystalline carbonates and cements.