Late Permian reefs of the Capitan complex, west Texas; the Magnesian Limestone, England; Chuenmuping reef, south China; and elsewhere contain anomalously large volumes of aragonite and calcite marine cements and sea-floor crusts, as well as abundant microbial precipitates. These components strongly influenced reef growth and may have been responsible for the construction of rigid, open reefal frames in which bryozoans and sponges became encrusted and structurally reinforced. In some cases, such as the upper biostrome of the Magnesian Limestone, precipitated microbialites and inorganic crusts were the primary constituents of the reef core. These microbial and inorganic reefs do not have modern marine counterparts; on the contrary, their textures and genesis are best understood through comparison with the older rock record, particularly that of the early Precambrian. Early Precambrian reefal facies are interpreted to have formed in a stratified ocean with anoxic deep waters enriched in carbonate alkalinity. Upwelling mixed deep and surface waters, resulting in massive seafloor precipitation of aragonite and calcite. During Mesoproterozoic and early Neoproterozoic time, the ocean became more fully oxidized, and seafloor carbonate precipitation was significantly reduced. However, during the late Neoproterozoic, sizeable volumes of deep ocean water once again became anoxic for protracted intervals; the distinctive "cap carbonates" found above Neoproterozoic tillites attest to renewed upwelling of anoxic bottom water enriched in carbonate alkalinity and 12C. Anomalous late Permian seafloor precipitates are interpreted as the product, at least in part, of similar processes. Massive carbonate precipitation was favored by: 1) reduced shelf space for carbonate precipitation, 2) increased flux of Ca to the oceans during increased continental erosion, 3) deep basinal anoxia that generated upwelling waters with elevated alkalinities, and 4) further evolution of ocean water in the restricted Delaware, Zechstein, and other basins. Temporal coincidence of these processes resulted in surface seawater that was greatly supersaturated by Phanerozoic standards and whose only precedents occurred in Precambrian oceans.