The present study is the first report of a detailed analysis of the frequency of Fusarium and genera related to Fusarium colonizing the root zone of clovers and grasses growing in a permanent meadow established on peat-muck soil in a post-bog habitat. The isolation of fungi was carried out on the Nash and Snyder medium with the plate dilution method. The taxonomic identification of the collection of pure fungal cultures was based on morphological features revealed by macroscopic and microscopic observations. The species dominance coefficients, Marczewski–Steinhaus and Simpson species diversity index were calculated. Eight Fusarium complexes were distinguished. The distribution of the Fusarium population was uneven, which was generally reflected in a higher frequency of the F. oxysporum species complex in the clover root zone and M. nivale, F. avenaceum from the Fusarium tricinctum species complex, and F. culmorum from the F. sambucinum species complex in the grass root zone. The highest similarity of fungi was determined in the rhizoplane and the endorhizosphere. The highest species diversity and the highest population size were determined in the rhizosphere soil. The fertilization treatment reduced the growth rates in the Fusarium sensu lato and in genera related to Fusarium, as evidenced by the decrease in the total abundance and species richness. The root colonization by the Fusarium, especially the F. oxysporum species complex, was not accompanied by plant pathologies, which suggests a saprotrophic and endophytic rather than parasitic character of the relationships with the plant host