The late Ordovician Soom Shale of South Africa contains exceptionally preserved fossils of several taxa, the soft tissues of which are uniquely composed of clay and alunite group minerals. In addition, originally phosphatic brachiopod shells and conodont elements have been replaced by clays. Sub-cellular structural details of conodont muscle tissues are faithfully replicated by the clay minerals. Geochemical analyses have constrained interpretation of the conditions in the sediment and bottom waters of the Soom Shale basin during deposition and early diagenesis. Anoxic-euxinic conditions prevailed with low carbonate and iron concentrations in the sediment; hence there was no mechanism to buffer or fix H2S produced by organic matter decomposition. Under low pH conditions and in the presence of cations, organic substrates would have had an affinity for colloidal clay minerals and may have acted as templates, controlling the absorption of clay minerals which eventually completely replaced them. An initial phase of mineralization involving phosphate, followed by its replacement by clay minerals, is unlikely because the low pH conditions in the sediment would have been inimical to phosphate concentration, and the high fidelity of some soft tissue replication militates against two phases of replacement.