Microbial communities in roots, rhizoplane, rhizosphere soil and non-rhizosphere soil in potato were compared in organic and integrated production systems in 2005–2007. Identification of microorganisms was based on morphotyping. The density (number of colony-forming units in a sample) of Fungi and Oomycota was significantly greater in the integrated system. Greater densities of Arthrobacter and Streptomyces occurred more often in organic and integrated systems, respectively. The dominant fungal taxa (with frequency >5% in at least one habitat) included Aspergillus, Clonostachys + Gliocladium, Colletotrichum coccodes, Fusarium + Gibberella + Haematonectria + Neonectria, Gibellulopsis nigrescens, Paecilomyces, Penicillium, Phoma and Trichoderma. The subdominant taxa (with frequency 1–5%) included species from 16 genera. In the rhizoplane, rhizosphere and non-rhizosphere soil, the total density of pathogens was greater in the organic system, and of antagonists in the integrated system. Dominant pathogens, that is, C. coccodes, Fusarium culmorum, Haematonectria haematococca and G. nigrescens, and dominant antagonists, that is, Clonostachys + Gliocladium and Trichoderma, occurred at greater density in the organic system. Subdominant pathogens, that is, Alternaria + Ulocladium, Pythium and Thanatephorus cucumeris, and subdominant antagonists, that is, Mortierella and Umbelopsis vinacea, occurred at significantly greater density in the integrated system. Incidence of sprout rot was more frequent in the organic system, and of Fusarium dry rot and black scurf in the integrated system. The organic system provided a less disease-suppressive environment than the integrated system and resulted in smaller potato yield. An integrated system of potato production based on 4-year rotation, white mustard as a cover crop, inorganic fertilizers including ammonium nitrate and chemical control of insects and diseases may be promoted in Poland.