Fully troglobitic pseudoscorpions are rare in the Afrotropical Region, and we explored the identity and phylogenetic relationships of specimens of a highly modified troglobite of the family Gymnobisiidae in the dark zone of the Wynberg Cave system, on Table Mountain, South Africa. This large pseudoscorpion – described as Gymnobisium inukshuk Harvey & Giribet, sp. nov. – lacks eyes and has extremely long appendages, and has been found together with other troglobitic fauna endemic only to this cave system. Phylogenetic analyses using the nuclear ribosomal genes 18S rRNA and 28S rRNA and the mitochondrial protein-encoding gene cytochrome c oxidase subunit I unambiguously place the new species with other surface Gymnobisium from South Africa. This placement receives strong support and is stable to analytical treatments, including static and dynamic homology, parsimony and maximum likelihood, and data removal for ambiguously aligned sites. This species is the first troglobitic species of the family and one of the most highly modified pseudoscorpions from the Afrotropical Region.