The results of molecular identification of toxigenic Fusarium spp. in local tomato varieties at some vegetative phases are presented. F. oxysporum, F. verticillioides, F. proliferatum, F. avenaceum, F. equiseti, F. solani were found at different stages of tomato development. Sequences of FUM gene cluster involved in the synthesis of Fumonisin B1 and Polyketide synthase (PKS13) gene sequences involved in the synthesis of Zearalenone were revealed in some tomato varieties infected by certain toxigenic Fusarium species.