The results of molecular phylogenetic studies based on the sequencing of matK gene and trnG-R intergenic spacer of the chloroplast DNA and analysis of the concatenated data of these loci of North Asian representatives of the Cystopteridaceae family are presented. In the genus Gymnocarpium, a dryopteris-clade was distinguished including species without glandular pubescence of fronds – Gymnocarpium dryopteris. Species having glandular pubescent fronds have formed the robertianum-clade (G. robertianum and G. fedtschenkoanum), and 2 subclades, including G. continentale, G. jessoense, and G. tenuipes. In the genus Cystopteris, the analysis confirmed the separation of C. montana from other Cystopteris species, and the separation of C. sudetica from the C. fragilis-complex. This advocate the recognition of monotypic genus Rhizomatopteris including Rh. montana (≡Cystopteris montana), and allows to recognize the section Khokhrjakovia (with C. sudetica) within the genus Cystopteris. This analysis did not allow to separate the species of the type subgenus Cystopteris (C. fragilis-complex) from each other.