The analysis included soil that represented the type of organic muck soils. The study involved the levels created by the muck and the organic layer formed by a mule track. The aim of the study was to determine changes in the structures of fungal communities micromycetes, which were received from organic muck soil in two subsequent years. The authors have attempted to clarify the relationship between soil organic, which was the process of humification and mineralization of organic matter, and communities of fungi colonizing that organic soil. The method for the isolation of fungi micromycetes selected Warcup soil tiles, which was modified by Mańka. The similarity between the communities of fungi determined using Jaccard coefficient. In total 153 colonies and 31 species of fungi micromycetes were obtained. The similarity between the communities of fungi in the soil in the subsequent two years of research, was of a different level. The highest similarity, amounting to 50%, showed a fungal communities colonizing the organic layer formed by a mule track. In 2013 community inhabiting unchanged layer of silt did not have in common with any of the communities of fungi present in organic soil that was sampled in 2012. The results allow to conclude that the analyzed fungi micromycetes are unstable in its qualitative structure. Even small changes in habitat contribute to the formation of communities with different quality characteristics (species composition) are also quantitative – turnout rates of the individual species and all communities. This affects low similarity between communities of fungi inhabiting different organic soils in a research year as well as in subsequent years.