Resumo. Changes in the management systems for the cultivation of different forest stands and the use of species rotation can lead to alterations in the quality of soil organic matter (SOM) and plant residuede position. This study evaluated the stage of decomposition and the contribution of plant and microbial origin for SOM through biomarkers, such as lignin-derived phenols, carbohydrates and amino sugars incontinuous shortrotation eucalypt (Eucalyptus urophylla x Eucalyptus grandis hybrid) (seven years) compared to a rotation system including acacia (Acacia mangium Willd.) after short-rotation eucalypt; and long-rotation eucalypt(24 years). A native vegetation (Atlantic Forest) was used as a reference for the original site condition representative for the northern coast of Espírito Santo state. To do so, we estimated the content of totalorganic C (TOC), total N (TN) and the contents of lignin-derived phenols (VSC), the carbohydrates and the amino sugars derived from soil microorganisms, and acids/aldehyde ratio of groups vanilil ((Ac/Al)vanilil) and syringyl ((Ac/Al)syringyl) of the lignin, hexoses/pentoses (H/P) ratio of carbohydrates, besides glucosamine/ muramic acid (Gluc/Ac. Mur) and glucosamine/galactosamine (Gluc/Gal) ratios for soil and litter samples. The results indicated that litter of the continuous short-rotation eucalypt has greater drymass, lignin (VSC) and carbohydrates contents, C/N and VSC/N ratios; a similar proportion of coarse litter to fine litter and C content, but a lower N content in comparison to the species rotation system that includes the leguminous acacia. In the soil, acacia cultivation increases C, N and carbohydrates content, widened the acid/aldehyde ratio of vanilil groups of lignin and the glucosamine/muramic acid ratio of amino sugars derived from microbial activity. The longer rotation of eucalypt (24 years) increased C content and decreased the VSC/N ratio in SOM compared to the continuous short-rotation eucalypt, but still having C and N content lower than in soil of acacia and native forest. The smallest Ac/Al ratio of lignin-derived phenols in soils cultivated with eucalypt (in long and short-rotation) indicates that the SOM is in less advanced stage of decomposition (humification) than in the soil cultivated with acacia, and that under native forest. In soils under acacia, followed by that of short-rotation eucalypt, the higher glucosamine/muramic acid ratio suggested a greatercontribution of fungi in SOM cycling, whereas in the native forest and long-rotation eucalypt there is greater abundance of bacteria-derived compounds. Overall, the results indicate that there was a recovery in the quality of the soils cultivated with eucalypt for a longer rotation and also with acacia in relation to the continuous short-rotation eucalypt.