Fusarium head blight (FHB) is a disease of small-grain cereals and corn caused by a complex of fungal species of the genus Fusarium. The disease reduces the yield and quality of seeds and results in the accumulation of various mycotoxins which cause a variety of toxic effects on humans and livestock. Beauvericin (BEA) and enniatins (ENs) are a group of toxins with antimicrobial, insecticidal and phytotoxic activities produced mainly by F. avenaceum, F. poae and F. tricinctum. In this study, primer sets were designed that were targeted to esyn1 gene homologs encoding multifunctional enzyme enniatin synthetase. Primers used in multiplex PCR amplified products from the FHB species reported to produce (ENs) and/or BEA. The use of the marker developed on asymptomatic wheat seed samples originating from Northern and Southern Poland demonstrated that all samples were positive for the presence of potential enniatin-producing Fusarium species.