Soil organic matter is composed of a variety of materials existing along a continuum of extent of decomposition. Computer models that simulate soil organic matter dynamics have been developed using conceptual pools of carbon that vary in there relative rates of decomposition. The Roth-C soil carbon model has been calibrated to accept and model methodologically defined fractions of soil organic matter (particulate organic matter, humus, and charcoal). This model has been incorporated into the FullCAM model being used in the National Carbon Accounting System for Australia. The distribution of carbon and nitrogen in the particulate, humus and charcoal fractions of soils from crop rotation trials located in the Australian Mallee at Waikerie, SA and Euston, NSW was quantified in this study. At each site three rotations representative of district practice and two more intensive cropping systems were included. The amounts of C and N associated with the various soil organic matter fractions was significantly influenced by the applied crop rotations. The ability of the FullCAM model framework to quantify carbon and nitrogen dynamics in the crop rotations at each site will be examined by comparing simulated outputs with soil and agronomic measurements.