The Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including T. rubrum sensu stricto and T. violaceum, as well as other less well established or debatable taxa like T. soudanense, T. kuryangei and T. megninii. We aimed to describe genetic lineages in Russian T. rubrum sensu stricto, to find whether these lineages possess specific characteristics and to identify factors, shaping the population structure. We assessed polymorphism of 12 simple sequence repeat (SSR, or microsatellite) loci and TERG_02941 protein-coding gene in 70 T. rubrum isolates and also performed phylogenomic analysis. In both cases, two genetic lineages were found. The analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22-48% of the variability was between groups within T. rubrum. The pattern of phylogenetic changes in polymorphic protein-coding loci and SSR typing results revealed the pressure of strong directional selection, but its sources remained elusive. Our results suggest that Russian population of T. rubrum consists of two cosmopolitan genetic lineages, with no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression and urease activity.HighlightsRussian population of fungal pathogen Trichophyton rubrum is formed by two global genetic lineagesPopulation structure in T. rubrum can be studied by improved microsatellite typing assay along with SNP typing and whole genome sequencingIn T. rubrum, there is seemingly no association between genetic lineages and types of infection, places of geographic origin, aldolase gene expression and urease activityIn T. rubrum, microevolution is driven by strong directional selection of yet unknown nature

Trichophyton rubrum is an ascomycete from the order Onygenales. It is prevalent fungus of medical importance in most countries due to its major contribution to the aetiology of toenail onychomycosis and foot skin mycosis. 1 Trichophyton rubrum sensu stricto is a part of species group, which also includes T violaceum and T soudanense along with several forms, potentially deserving species status. All of these can be differentiated by ribosomal DNA internal transcribed spacer (ITS) region sequences. 2-6 Statistical analysis of genetic