Pathogenic fungi are the cause of various diseases of crops. Phytopathogens infect seeds as well as the host-plants in the course of the whole duration of their ontogenesis. Plants are infected when grown in greenhouses or in open fields by a single causal agent or several pathogenic fungi. In current study, a nested PCR protocol was applied for identification of tomatoes’ infection. An infestation with Alternaria spp. and Myrothecium roridum in the lowest leaves on the stem was stated using molecular diagnostics. The ‘Tomis’ and ‘Mary Gratefully’ tomato cultivars were used in current study. Alternaria spp. was iden-tified in each of the samples. The pathogen’s species was defined. Myrothecium roridum infested 10 sam-ples of the ‘Tomis’ genotype and 11 samples of the ‘Mary Gratefully’ genotype of the 12 samples.