Alternaria and Fusarium are two genera of worldwide-distributed fungi. Many of them are common  plant pathogens that cause significant economical loses. They have a wide range of host plants and  cause severe diseases known as alternariosises and fusariosises. Alternaria species under favorable  conditions can cause loses of 50% to 90% of total yield.  Most  common  symptoms  are  stem   cankers,  leaf  and  stem  lesions,  chlorosis.  In addition, Fusarium and Alternaria species can  affect yield during storage causing rot and quality  alteration.  Many  species  also  can  produce   mycotoxins.  These  are  secondary metabolites that affect human health and cause toxicosises,  immune supression, tissue necrosis and even can induce carcinogenesis. So far, mycotoxin  concentration in food and primal sources for food production is inder strict reglamentation in many  countries. The main object of this paper was to investigate distribution of Fusarium and Alternaria species   in  winter  wheat  plants  focusing  on  species  that  are  known  as  producents  of mycotoxins.  Two local varieties of wheat («Moldova 79» and «L-18») were analysed. At early phases of vegetation  most plants of both varieties were infected with Alternaria spp. Fusarium spp. was presented with  less frequency on leaves, yet was identified in about  100%  of  root  samples.  At  early  phases  of  vegetation,  most  plants  were  infected  with  Alternaria spp., while Fusarium spp. was identified only in root system. Developing ears were  absent of fungi. Fusarium oxysporum was identified in roots and absent of aerial parts of the wheat  plants, while F. verticillioides and F. avenaceum were identified on leaves and ears. Mass  infection was observed during flowering phase and percentage of infected plants was similar for  both varieties. No conclusion about resistance to fungal pathogens could be done due to the fact  that none of the cultivars showed symptoms of infection.