Investigations concerned the horseradish roots originating from a strict field experiment conducted in 2010-2011, in which chemical protection using: Topsin M 500, Dithane 455 SC, Penncozeb 80WP and Amistar 250 SC and non-chemical protection by Polyversum WP biopreparation and biotechnological preparations: Biosept 33SL, Bioczos BR and Biochikol 020 PC were applied. Irrespectively of the applied protection, a total of 755 fungi colonies of 14 genera were separated from the horseradish roots. The fungi classified to Fusarium genus were isolated most frequently, making up 35.7% of the total isolate number, subsequently Verticillium dahliae - 15.85%, Alternaria alternata - 6.09% and Pythium irregulare - 5.16%. The fungi community isolated from the horseradish roots from the object protected by synthetic fungicides was characterised by a greater number of fungi settling them, but at the same time it was less diversified regarding the species in comparison with the roots under biological protection. Chemical protection generally favoured the roots settling by pathogenic fungi (83.9%), whereas biological preparations favoured antagonistic species, such as Trichoderma harzianum and Trichoderma viride, which were not present in the objects under chemical protection.