Resumo. The pursuit of sustainable systems of soil management has led researchers to develop new techniques of cultivation. Among them, studies with forest species able to fix atmospheric N2 and increase C and N stocks in labile and stable soil organic matter (SOM) stand out in Brazil. The study aimed to evaluate changes in stocks of C and N in fractions of humic substances, light fraction of SOM and microbial biomass in soils of short-rotation Eucalyptus “urograndis”, long rotation plantations and stands of Acacia mangium which succeeded short rotation eucalyptus monoculture, in comparison to the soil of native forest (Atlantic Forest). It was obtained the total organic carbon (TOC) and total nitrogen (TN) stocks, C and N stocks in the fractions of humic substances (fulvic acid fraction-AF, humic acid fraction-HA and humin fraction-H), C and N in light fraction of SOM (C-LOM and N-LOM) and C and N microbial biomass (CMB and N-MB). The results indicated that the short rotation eucalyptus cultivation reduced total organic carbon stocks, total nitrogen, C and N in the humic substances, and N storage in the microbial biomass compared to Acacia mangium soil. The cultivation of Acacia mangium and the increase of the eucalyptus rotation time increased stocks of C and N of the labile (C-LOM, N-LOM and C-MB) and stable fractions (C and N in humic substances) indicating a significant recovery of their stocks to levels approaching those original (native), and higher than stocks obtained in the soil of short rotation eucalypt.