The molecular characterization of Boeremia strasseri (Moesz) Gruyter et Verkley (basionym Phoma strasseri Moesz) isolates from peppermint crops grown in south-eastern and central Poland was studied using the Random Amplified Polymorphic DNA (RAPD) -PCR technique. Tests were performed using randomly selected primers. DNA profiles obtained using five primers proved to be useful in determining the genetic variability among B. strasseri genotypes. Molecular analysis of four loci: (i) rDNA internal transcribed spacer region (ITS1, 5.8S, ITS2); (ii) LSU (partial large subunit DNA 28S); (iii) tub 2 (gene region of β-tubulin); (iv) act (gene region of gamma-actin) proved that the actin gene is the most suitable DNA barcode for the accurate and rapid identification B. strasseri species.