Current paper outlines the infestation of 'Tomis' tomato variety seeds with Alternaria spp.,   Fusarium  spp.  and  Myrotheciu  roridum  phytopathogens.  Using  nested-PCR  on DNA extracted from  3-day germinated seeds with 2% SDS extraction buffer, with primer mix for Alternaria and  Myrothecium roridum pathogen spread in seed DNA samples was obtained. Alternaria spp. was  identified with primers to II second largest subunit (rpb 2) from  NCBI  nucleotide  database   (GenBank).  For  Myrothecium  roridum  identification primers to !TS small subunit ribosomal RNA  gene sequence were used. In 4 of 9 analyzed DNA samples Alternaria spp. was identified. Myrothecium  roridum was identified in a single sample. In the same sample a mixed infection of Alternaria spp.  and Myrothecium roridum   was   identified.   For   Alternaria   spp.   corresponded   a   160   bp    band   on electroforegramm generated by specific primers. A 305 bp amplicon corresponded for  Myrothecium roridum. Same  DNA  was  analyzed  for  presence  of  Fusarium  pathogens.  Fusarium  spp.  was identified  in tomato DNA samples via nested-PCR with primers to final elongation factor TEFJ gene sequence  from NCBI nucleotide database (GenBank). In 4 samples Fusarium fungi were identified. Second round  primer pair generated a 300 bp. Mentioned amplicon was visualized on electroforegramms of  corresponding samples. As a result, in 'Tomis' seeds Alternaria spp., Fusarium spp. and Myrothecium roridum phytopathogens  were identified. Alternaria spp. and Fusarium spp. infection rate was 44%. Myrothecium roridum was  identified in 11% of the analyzed samples. In 2 samples simultaneously were identified Fusarium  spp. and Alternaria spp. (22% infection rate). Mixed Alternaria spp. and Myrothecium roridum  infection was identified in one sample (11%). Upon obtained data of seed DNA analysis a conclusion about phytopathogen genera in seed   material    was   made.   In   DNA   samples   Alternaria   spp.,   Fusarium   spp.   and Myrothecium roridum  were identified. Seed infection rate was 64%. Seed analysis for pathogen infestation using molecular methods proves to be a modern and  highly   effective  method.  This  approach  gives  the  opportunity  to  evaluate  the phytosanitary risks of seed material using minimum quantity of vegetal samples.