Male secondary genitalia (pedipalps) are useful characters for species discrimination in most spider families. Although efforts have been made to establish pedipalp sclerite homologies, there are still many inconsistencies in their use. The majority of the morphological characters used to reconstruct the linyphiid phylogeny address male genitalic variation; these inconsistencies may affect the phylogeny and our understanding of linyphiid evolution. Stemonyphantes Menge, 1866, has been hypothesised to be sister to all remaining Linyphiidae. However, despite the basal position of Stemonyphantes, its pedipalp sclerite homologies are not well understood and, along with its monophyly, have never been thoroughly tested in a phylogenetic context. We tested the homology of tegular and radical structures of five Stemonyphantes species to the known linyphioid and araneoid sclerites. All minimum-length trees found under all analytical methods used support Stemonyphantes monophyly and its placement as the sister group to all other Linyphiidae. Our study suggests that Stemonyphantes, unlike any other linyphiids, does have homologues of the araneoid median apophysis and conductor. As Stemonyphantes is the sister group of all other linyphiids, resolving its pedipalp sclerite homologies is critical for understanding sclerite homologies and the phylogeny of the entire family.