A phylogenetic analysis of the genera of Cyphophthalmi is undertaken by studying 32 morphological characters in 43 species representing all families and most genera. The analysis is complemented with a molecular analysis using 18S rRNA and 28S rRNA sequence data of twelve cyphophthalmid species representing ten genera. The Cyphophthalmi are monophyletic, as are the families Stylocellidae and Pettalidae. However, the families Sironidae, Ogoveidae, and Neogoveidae are not monophyletic. Relationships among families need more data, but molecular characters strongly support the monophyly of Troglosironidae Neogoveidae. Rooting the cyphophthalmid tree by using sequence data of one Eupnoi, one Dyspnoi, and one Laniatores results in two alternatives, one proposing a sister group relationship of Stylocellidae to the remaining taxa, or alternatively Pettalidae (with Suzukielus?) as sister group of the remaining cyphophthalmids. The position of Troglosiro, Suzukielus, Metasiro, Huitaca, and the epigean “Neogovea” mexasca are re-evaluated and discussed.
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