There are few quantitative techniques in use today for palaeoecological reconstruction in terrestrial depositional systems. One approach to such reconstructions is to estimate the proportion of C3 to C4 plants once present at a site using carbon isotopes from paelaeosol carbonates1-3. Until now, this has been hampered by an inadequate understanding of the relationship between the carbon isotopic composition of modern soil carbonate and coexisting organic matter. Here we have found that the two systematically differ by 14-16% in undisturbed modern soils. This difference is compatible with isotopic equilibrium between gaseous CO2, and aqueous and solid carbonate species in a soil system controlled by diffusive mass transfer of soil CO2 derived from irreversible oxidation of soil organic matter. Organic matter and pedogenic carbonate from palaeosols of Pleistocene to late Miocene age in Pakistan also differ by 14-16%. This indicates that diagenesis has not altered the original isotopic composition of either phase, thus confirming their use in palaeoecological reconstruction