The chromosome number and phylogenetic position of the monotypic eusporangiate genus Mankyua (Ophioglossaceae), which shares peculiar morphological characteristics with Ophioglossum s.l. and Helminthostachys, were determined. Meiotic and mitotic chromosome observations of Mankyua show n = 130 and 2n = ca. 260, suggesting that the base number of this genus is x = 130, which is a new finding and the highest base number reported so far for Ophioglossaceae. The molecular phylogenetic trees derived from nucleotide sequence variation of rbcL and matK genes differ in terms of the phylogenetic position of Mankyua. The molecular phylogenetic trees based on combined data sets of rbcL and matK suggest that Mankyua might be the earliest-diverging lineage of Ophioglossaceae.