Agroforestry systems can play a major role in the sequestration of carbon (C) because of their higher input of organic material to the soil. The importance of organic carbon to the physical, chemical, and biological aspects of soil quality is well recognized. However, total organic carbon measurements might not be sensitive indicators of changes in soil quality. Adoption of procedures that can extract the more labile fraction preferentially might be a more useful approach for the characterization of soil organic carbon resulting from different soils. This study aimed to evaluate organic carbon (C) fractions distribution in different soil layers up to 50 cm depth in two soil orders under cacao (Theobroma cacao) agroforestry systems (AFS) in Bahia, Brazil. Soil samples were collected from four depth classes (0-5, 5-10, 10-30 and 30-50 cm) under two cacao agroforestry systems (30-year-old stands of cacao with Erythrina glauca, as shade trees) in Latosol and Cambisol, in Bahia, Brazil. The determination of oxidizable carbon by a modified Walkley-Black method was done to obtain four C fractions with different labile forms of C (fraction 1: labile fraction; fraction 2: moderate labile fraction; fraction 3: low labile fraction and fraction 4: recalcitrant fraction). Overall, at two cacao AFS, the C fractions generally declined with increase in soil depth. The C fractions 1 and 2 were 50% higher on upper layers (0-5 and 5-10 cm). More than 50% of organic C was found in more labile fraction (fraction 1) in all depths for both soils. High value of C fraction 1 (more labile C)-to-total organic C ratio was obtained (around 54-59%, on Latosol and Cambisol, respectively), indicating large input of organic matter in these soils.