This article describes the application of the classical PCR method for the diagnosis of the soybean bacterial blight pathogen Pseudomonas savastanoi pv. glycinea in seeds. Two methods for pathogen isolation from infected soybean seeds, five methods for DNA extraction and two master mixes for preparation of reaction mixture were investigated. The use of a PCR-based test system with oligonucleotides specific for the coronaphacate ligase (cfl) gene allowed the diagnosis of the soybean bacterial blight pathogen in seeds at a concentration of 2 × 103 CFU/ml. The analytical sensitivity of the protocol was 97.4% of 37 closely related and other bacteria tested. Product yield (amplicon peak area) was shown to be highest (645.0 units) when DNA was isolated using the Proba-GS kit, the master mix 5x MasDDDTaqMIX-2025 and the primers PsgFOR-1 and PsgREV-2 were used at 10 pM per reaction (25 μL).