The phylogenetic relationships of the major lineages of the arachnid order Pseudoscorpiones are investigated for the first time using molecular sequence data from two nuclear ribosomal genes and one mitochondrial protein-encoding gene. The data were analyzed using a dynamic homology approach with the new program POY v.4 under parsimony as the optimality criterion. The data show monophyly of Pseudoscorpiones as well as many of its superfamilies (Feaelloidea, Chthonioidea, Cheiridioidea and Sternophoroidea), but not for Neobisiodea or Garypoidea. Cheliferoidea was not monophyletic either due to the position of Neochelanops, which grouped with some garypoids. In all the analyses, Feaelloidea constituted the sister group to all other pseudoscorpions; Chthonioidea is the sister group to the remaining families, which constitute the group Iocheirata sensu Harvey-a clade including pseudoscorpions with venom glands within the pedipalpal fingers. This phylogenetic pattern suggests that venom glands evolved just once within this order of arachnids.