Sri Lanka harbours an exceptionally high diversity of goblin spiders (family Oonopidae), with 45 currently recognised species across 13 genera, of which 38 are endemic. In this study, we present a molecular phylogenetic analysis based on two nuclear ribosomal markers (18S and 28S rRNA), incorporating 28 species from eight genera: Aprusia, Brignolia, Ischnothyreus, Opopaea, Orchestina, Pelicinus, Silhouettella, and Xestaspis. These taxa were analysed in the context of the existing global phylogeny, enabling both regional and broader evolutionary comparisons. Our results reveal that several genera, particularly Brignolia, Opopaea, and Ischnothyreus, are paraphyletic, highlighting the need for taxonomic revision. Endemic clades such as Aprusia, Brignolia, and Xestaspis show strong evidence of recent, within-island speciation and microendemism. The genus Orchestina is recovered as monophyletic, with Sri Lankan species forming a distinct clade. The findings support the hypothesis that reduced body sclerotisation is a plesiomorphic trait in oonopids. Overall, the study underscores the exceptional microendemism and evolutionary distinctiveness of Sri Lanka's oonopid fauna, likely driven by both ecological isolation and in situ speciation. However, given the incomplete representation of Indian and Southeast Asian taxa, and limited molecular sampling, further studies incorporating broader taxon and gene sampling are needed to fully resolve the origins and diversification of this ecologically important spider family.