The relationships between the genera in Gnathostomulida were investigated in a computerized cladistic analysis. The data matrix comprised 55 morphological characters of sensory structures, the reproductive systems, and the hard mouthparts. The cladistic analysis produced four almost identical most parsimonious trees. The four trees differed by having different topologies within the family Gnathostomulidae. Based on the obtained trees, the following was concluded: (1) Filospermoidea and Bursovaginoidea are both monophyletic; (2) Scleroperalia is paraphyletic; (3) all known families except Onychognathiidae (Sterrer 1972) are monophyletic; (4) Onychognathiidae emend. comprises the genera Nanognathia, Onychognathia, Rastrognathia, Valvognathia and Vampyrognathia; (5) Paucidentulidae and Onychognathiidae emend. branch off in the lower part of Bursovaginoidea; (6) the following two clades are monophyletic and appear as sister groups: Problognathiidae-Gnathostomulidae-Austrognathiidae and Gnathostomariidae-Goannagnathia-Mesognathariidae-Clausognathiidae- Agnathiellidae. Based on the character optimization it was suggested that the gnathostomulid jaw evolved from a relatively simple ancestral jaw belonging to the compact type or the open lamellar type. The fused lamellar type evolved from the open lamellar type. The ancestral dentarium resembled the arc type and evolved along two different evolutionary paths into the basket type and the row type.