We conducted phylogenomic analyses of Rakaia, a genus of mite harvestman (Arachnida, Opiliones, Cyphophthalmi) from New Zealand, based on sequence capture of ultraconserved elements (UCEs), which are exonic in origin in arachnids. Rakaia is the most speciose and widespread mite harvestman genus in New Zealand. Previous efforts to understand phylogenetic relationships within this group have used a standard Sanger sequencing approach, and have been restricted in terms of taxonomic sampling and number of loci sequenced. UCEs target capture allowed sequencing of several important historical museum specimens, which was not possible with Sanger sequencing due to DNA degradation. We sequenced UCEs from forty-seven Rakaia specimens belonging to seventeen named species and six undescribed species, in a first attempt at using next-generation sequencing techniques for New Zealand mite harvestmen at the species level. Morphological and geographical data were used integratively with our phylogenomic results to identify four new species; we successfully included a thirty-five-year-old specimen in our phylogeny, and monophyly was supported in two putative new species. We discuss ways in which we could improve this phylogeny, namely the use of more individuals per species, refined post-sequence analyses, and the development of a clade-specific probe set. We identify future directions for utilizing these high-resolution phylogenies based on UCEs to test long-disputed biogeographical hypotheses in the context of Gondwanan vicariance.