The abundance and species composition of fungi colonizing grain of spring wheat cvs. 'Koksa' and 'Torka', grown in the conventional and organic farming systems, was assessed in 2004-2006. More colonies of Alternaria alternata, Aureo- basidium pullulans, Botrytis cinerea and Fusarium spp., Gibberella spp. were isolated from wheat grain obtained from conventional farms. Intensive chemical control did not reduce the abundance and species diversity of Fusarium spp., Gibberella spp. A considerably higher number of Epicoccum nigrum colonies were isolated in the organic farming system, as compared with the conventional system.