Systematic position of the genus Habrodon was considered quite differently by various authors – it was placed in Habrodontaceae, Fabroniaceae, Myriniaceae, Leskeaceae, and Pterigynandraceae. The analysis of nucleotide sequence data (chloroplast trnL-F region and nuclear ITS1 & ITS2) was undertaken to elucidate Habrodon relationships. This analysis revealed quite distinct position of Habrodon from Leskea and Myrinia, and found Habrodon within a paraphyletic grade with Plagiotheciaceae (sensu lato, cf. Hedenas, 1987; Pedersen & Hedenas, 2002) and Fabronia and sometimes also with Pterigynandrum. The acceptance of the monogeneric family of Habrodontaceae Schimp. is suggested. Other inferrings from analysis support the segregaion of Iwatsukiella from Habrodon, but do not support the monophyly of the family Leskeaceae, which seems need to be strongly reconsidered. Pterigynandraceae sensu Buck & Goffinet (2000), represented in our analysis by all five genera (i. e. Habrodon, Myurella, Heterocladium, Iwatsukiella, and Pterigynandrum) were also found not monophyletic. Topology of tree obtained from molecular data shows certain correlation with some morphological characters, especially pattern of distribution of foliose structures around juvenille branch primordia. Also, Habrodon and neighboring members of its paraphyletic grade all have uniqe structure of uniseriate axillary gemmae.