Backgrounds and aims Soils are known to influence the survival and the biocontrol activity of Pseudomonas bacteria. However, few studies have focused on the development of the phytopathogenic fungus Fusarium culmorum under various soil conditions and its interactions with the antagonistic microflora. The aims of our research were to study the development of Fusarium culmorum and Pseudomonas fluorescens in two soils with different textures and on barley roots and to assess the influence of these soils in the growth, colonization capacity and interactions between the phytopathogen and the antagonist. Methods Development of F. culmorum and P. fluorescens was studied in dynamics on membranes in two nonsterile soils with different textures, as well as on barley roots. F. culmorum was identified by indirect immunofluorescent method, and P. fluorescens was visualised with the use of a gus-marked strain. Results P. fluorescens 2137gus suppressed considerably the mycelium growth and the macroconidia formation of F. culmorum in both soils. However, bacterium did not decrease considerably the density of the fungal mycelium on the surface of barley roots. On the contrary, the amount of the 2137gus was decreased considerably on roots in the light loamy soil in the presence of F. culmorum. Nevertheless, biocontrol effect of P. fluorescens 2137gus was expressed in the light loamy soil. There was no direct correlation between the mycelia density on membranes in soils and the amount of the fungus on roots at the beginning of colonization. The amount of the fungus on root surface did not correlate directly with the intensity of barley root rot. Conclusion The behaviour and interactions of F. culmorum and P. fluorescens depend on soil type and the habitat (soil or roots).