Intraspecies genetic variability of the medicinal dikaryotic polypore mushroom Fomitopsis pinicola was analyzed by using variable internal transcribed space (ITS) region of the ribosomal DNA gene cluster and the somatic compatibility test. The results revealed very low ITS sequence polymorphism among strains of F. pinicola from geographically distant origins (Russia, Finland, and France). Because of its conserved structure, the ITS region of the ribosomal DNA cluster can be proposed as a reliable molecular code for identifying and taxonomically verifying F. pinicola sensu stricto species. Four types of somatic incompatibility interactions were found in the Moscow population; 29 dikaryotic isolates revealed 27 somatically incompatible groups with an overall diversity index (HVC) of 0.782. Moderate antagonistic (somatically incompatible) interactions were predominant, with a frequency (p) of 0.56; strong antagonism with the heavily pigmented interaction zone was estimated as p = 0.35. These findings regarding the genetic diversity of natural F. pinicola isolates will assist further research and development of novel strains useful in food, medicine, and industrial applications.