Soils of the Cerrado have chemical, physical, and biological limitations for agriculture, which, associated with climate factors, contribute to their impoverishment. The maintenance and accumulation of soil organic matter are considered the best option of addressing this problem and to ensure a sustainable production. The purpose of this study was to evaluate different fractions of organic matter, and carbon and nitrogen contained in these compartments of a very clayey dystroferric Red Latossol under different crop rotations and at different depths under long-term no-tillage in Dourados, state of Mato Grosso do Sul. The experiment was arranged in a randomized block design with three replications, and the treatments in a 5x4 factorial design, with five crop rotation systems (1 - vetch + oat + oilseed radish/ soybean/ radish/ maize/ vetch + oats + radish/soybean; 2 - sunflower/ soybean/ vetch + oat + radish/ maize/ sunflower/ soybean; 3 -oat/ soybean/ sunflower/ maize/ oat/ soybean; 4 - vetch + oat/ soybean/ brachiaria/ maize/ brachiaria/ soybean; 5 - vetch/ soybean/ vetch/ maize/ vetch/ soybean), in four soil layers (0-5, 5-10, 10-15, 15-20 cm). Particle size was analyzed to determine the particulate fraction of organic matter (POM), and carbon (C-POM) and nitrogen (N-POM) in it. It was concluded that the levels and stock of C-POM, and nitrogen contents in the soil are not influenced by the different crop rotation systems. Crop rotation 4 increased the levels and stock of total organic carbon (TOC), carbon associated with soil minerals (C-MOM) and the total C/N ratio and total C/N ratio associated with soil minerals. The highest levels of TOC, C-POM, C-MOM, total nitrogen, N-POM and nitrogen associated with soil minerals (N-MOM) were found in the 0-5cm layer.