This study evaluated the comparative effect of a native N-fixing species and an exotic species (Pterogyne nitens and Eucalyptus urophylla, respectively) plantation on the organic carbon content of humic substances (HS) in a semi-arid soil, using native forest as a reference. Soil collections were performed at three depths of 0-10, 10-20 and 20-40 cm. Quantification of the humic substance fractions was performed by chemical fractionation, based on the differential solubility in alkaline and acid medium. Carbon (C) contents were determined by wet oxidation in acid medium. The C contents for the total humic substances when analyzing the 0-40 cm depth and the humine fraction showed inferior results in Pterogyne nitens plantation (PN) compared to native forest (NF) and Eucalyptus urophylla plantation (EU). The distribution of C in the humic fractions reflected the quantity and quality of the litter deposited by the forest cover. PN promoted lower carbon accumulation in HS, increased contribution of the most soluble fractions and reduced the most stable fractions of humic organic matter. In turn, EU did not provide major changes in the C contents and distribution in HS. The results indicated that the higher PN (a native N-fixing species) litter decomposition rates would provide a shorter time for organic matter stabilization. These results specifically contribute to a clearer understanding of the minute distinctions in soil organic matter quality observed between native and exotic species in semi-arid environments.