Black limestone clasts are present across the globe at modern and ancient subaerial exposure surfaces, and in intertidal and supratidal environments. These problematic clasts are particularly abundant at multiple subaerial exposure surfaces across southern Australia. The genesis of such exceptionally preserved clasts can be interpreted through universal fabrics across wide geographic regions and geologic ages. Regardless of location or age, all south Australian blackened clasts studied have a similar microstructure that is dominated by porous micritic laminae and chambered tubules. Such laminae are interpreted to represent calcified root cells and occur in two different varieties: 1) micrite-walled tubules with hollow centers that are thought to represent calcification in the rhizosphere or outer surfaces of the root, and 2) tubules consistent with calcification of both the medulla and cortex, which preserved medulla, cortex, and parenchymatic cells along with xylem vessels. Preserved root fabrics are present only in the blackest clasts and are consequently thought to be the main mechanism driving limestone blackening. The dark coloration in southern Australian clasts is derived from the impregnation of partially decayed terrestrial organic substances. These organic substances were trapped in the cellular structures of roots as they calcified and were subsequently prevented from further decay and oxidation. A threshold of approximately 7-weight % organic carbon is needed in the insoluble residue to produce the distinct black coloration in limestone. This process occurs at the base of slightly organic-rich humic soil profiles where they interact with underlying carbonate bedrock (B–C soil horizon). Roots both physically and chemically (through acid secretion) corrode the underlying limestone and provide the calcium bicarbonate needed in the root calcification process. Specific semiarid flora have the ability to calcify their cellular structures, which could explain why blackened clasts occur at only some unconformities. This result means that the formation of blackened clasts via root calcification and entrapment of organics relies upon specific conditions of semiarid plants and climate along with organic soils. Such conditions would be restricted to a specific climate regime and when combined with the new proposed blackening mechanism herein could help explain their limited distribution and occurrences worldwide.