After tumultuous revisions to the family-level systematics of Laniatores (the armored harvestmen), the basally branching family Phalangodidae presently bears a disjunct and irregular distribution, attributed to the fragmentation of Pangea. One of the curious lineages assigned to Phalangodidae is the monotypic Israeli genus Haasus, the only Laniatores species that occurs in Israel, and whose presence in the Levant has been inferred to result from biogeographic connectivity with Eurasia. Recent surveys of Israeli caves have also yielded a new troglobitic morphospecies of Haasus. Here, we describe this new species as Haasus naasane sp. nov. So as to test the biogeographic affinity of Haasus, we sequenced DNA from both species and RNA from Haasus naasane sp. nov., to assess their phylogenetic placement. Our results showed that the new species is clearly closely related to Haasus judaeus, but Haasus itself is unambiguously nested within the largely Afrotropical family Pyramidopidae. In addition, the Japanese ‘phalangodid’ Proscotolemon sauteri was recovered as nested within the Southeast Asian family Petrobunidae. Phylogenomic placement of Haasus naasane sp. nov. in a 1550-locus matrix indicates that Pyramidopidae has an unstable position in the tree of Laniatores, with alternative partitioning of the matrix recovering high nodal support for mutually exclusive tree topologies. Exploration of phylogenetic signal showed the cause of this instability to be a considerable conflict between partitions, suggesting that the basal phylogeny of Laniatores may not yet be stable to addition of taxa. We transfer Haasus to Pyramidopidae (new familial assignment). Additionally, we transfer Proscotolemon to the family Petrobunidae (new familial assignment). Future studies on basal Laniatores phylogeny should emphasise the investigation of small-bodied and obscure groups that superficially resemble Phalangodidae.