Fungal phytopathogens are responsible for significant losses in agriculture worldwide. Diagnosis of seed infestation by fungal strains causing plant diseases or producing toxins is important for sustainable agriculture. Since plants are always colonized by fungal strains there is a demand in approaches for reliable discrimination between harmless and hazardous fungi both in grains. We tested phytotoxic properties, mycotoxin production and colonization of wheat seedlings among 11 fungal isolated obtained from wheat grains of different varieties. The isolates were identified as Alternaria tenuissima, Alternaria infectoria, Bipolaris sorokiniana Alternaria arborescens, Alternaria alternata and Alternaria rosae. Strains A. tenuissima AB-F 72, A. arborescens AB-F 73, A. alternata AB-F 75, A. rosae AB-F 77 were producing phytotoxins inhbiting growth of wheat seedling. Four strains: B. sorokiniana AB-F 61, A. arborescens AB-F 73, A. alternata AB-F 74, A. rosae AB-F 77 were producing mycotoxins. Five strains A. rosae AB-F 77, A. tenuissima AB-F 76, A. infectoria AB-F 78 and A. infectoria AB-F 84 showed heavy colonization of wheat plantlets suggesting that these strains can be pathogenic to wheat. The results show that toxin production is not an obligatory characteristic for phytopathogenic strain, therefore using of proliferation of fungal strain in seedling tissue can be added as an additional test to seed quality evaluation.