The origin, structure, composition, and properties of soil humus horizons in functional zones of St. Petersburg have been studied. The radiocarbon age of organic matter in the humus horizons varies from 500 to 2700 years, which attests to the natural origin of humus. The structure of microbiomes in the humus horizons of soils under different plant communities has its specific features. The taxonomic structure of microbial communities at the phylum level reflects both genetic features of natural soils and the impact of anthropogenic factors, including alkalization typical of the studied urban soils. Tomographic studies have shown that the transporting system of humus horizons is less developed in the anthropogenically transformed soils in comparison with the natural soils. It can be supposed that the intensity of water and gas exchange in the anthropogenic soils is much lower than that in the natural soils. The fractional and group composition of humus in the urban soils is specified by the long-term pedogenesis, on one hand, and by the impact of metabolic products of the city and the factors of soil formation in the megalopolis, on the other hand. Bulk density of the humus horizon in the urban soils is higher than that in the natural soils; the portion of overcompacted humus horizons in the urban soils reaches 44%. Humus horizons of the lawns along highways are most contaminated with heavy metals: Pb, Zn, and Cu. There are no definite regularities in the distribution of major nutrients (NPK) in the humus horizons of anthropogenic soils.