Abstract: Genetic relationships between 27 Orthotrichum species of the subgenera Orthotrichum and Pulchella were reconstructed using the internal transcribed spacer regions 1 and 2, the chloroplast trnH-psbA region, and intron–exon splice junction (ISJ) and inter-simple sequence repeats (ISSR) markers. A phylogenetic analysis did not reflect the current division of the subgenus Pulchella into the sections Diaphana, Pulchella, and Rivularia. Species of the section Rivularia did not form a monophyletic group, and the only markers that indicated the distinctness of the section Pulchella were ISJ and ISSR. The most genetically diverse section was Diaphana, whose species were divided into several clades. The only proper phylogenetic unit was the subgenus Orthotrichum. The applied markers revealed the process of cryptic speciation in species of both subgenera.

Key words: ISJ, ISSR, ITS, molecular taxonomy, Orthotrichum, phylogeny, trnH-psbA.