The aim of this study was to examine the effect of 40-year differentated fertilization (mineral, organic, mineral-organic), crop rotation (4-field crop rotation with red clover and without legumes) as well as the 20-year soil tillage systems (mouldboard plowing, direct drilling) on soil microstructure. The study was based on three long-term field experiments located on the black earth (Mollic Gleysols) developed from light boulder loam. The content of soil microaggregates 1.0-0.05 mm was determined by wet sieving and the content of micro-aggregates <0.05 mm by pipette method. The content of soil micro-aggregates (Wd) was expressed as a proportion of micro-aggregates content in soil to soil particles content of the same size. The soil and plant cultivation systems significantly influenced the soil microstructure. Especially continuous use of direct drilling and manure fertilization as well as the crop rotation with red clover significantly limited the dispersion of soil on micro-aggregates <0.05 mm. These treatments simultaneously increased the content of micro-aggregate fractions >0.05 mm in the dispersed soil.