Recent phylogenetic studies of Opiliones have shown that Cyphophthalmi and Phalangida (= Palpatores Laniatores) are sister groups, but higher relationships within Phalangida remain controversial. Current debate focuses on whether Palpatores (= Caddoidea Phalangioidea Ischyropsalidoidea Troguloidea) is monophyletic or paraphyletic, with Ischyropsalidoidea Troguloidea (= Dyspnoi) being more closely related to Laniatores. The latter hypothesis was favored in recent combined studies of ribosomal DNA and morphology. Here higher relationships within Phalangida are examined using two nuclear protein-encoding genes, elongation factor-1α (EF-1α) and RNA polymerase II (Pol II), from 27 opilion species representing seven superfamilies. Cyphophthalmi was used as the outgroup. Nucleotide and inferred amino acid sequences were analyzed using maximum-parsimony and maximum-likelihood methods. All analyses recovered Palpatores as the monophyletic sister group to Laniatores with moderate to strong empirical support. Most palpatorean superfamilies were also recovered, but relationships among them were ambiguous or weakly supported. A monophyletic Palpatores was also obtained when EF-1α and Pol II sequences were analyzed together with 18S and 28S rDNA sequences.