ABSTRACT Molecular studies are often essential to infer phylogenetic relationships and biogeography in troglobiotic taxa, frequently characterised by convergent adaptations and cryptic species. Genetic analysis is a particularly useful tool in Dinaric karst, where palaeogeographic history complicates the interpretation of the evolutionary history of cave organisms. In this paper we estimate phylogenetic relationships in an entirely troglobiotic group of perceivable cirolanid isopods, inhabiting Dinarides and other Mediterranean regions, by a DNA-based approach, with a particular attention to the genus Sphaeromides. The originally more extensive genus Sphaeromides appears limited to S. raymondi in Southern France, while we suggest restoring the genus and name Trogloaega for the Dinaric taxa, previously attributed to Sphaeromides. The name and taxon Trogloaega have never been scientifically invalidated, just ignored. Results indicated that S. virei, formerly divided into three subspecies, consists of two or three distinct species, now named T. virei, T. mediodalmatina and T. montenigrina, the latter molecularly closer to T. mediodalmatina. The genus Trogloaega is genetically distant from Sphaeromides. Sphaeromides bureschi from Balkans (Bulgaria, Serbia) appeared closer to Trogloaega than to Sphaeromides. Our results contribute to the awareness that the isopod morphology is characterised by high level of homoplasy and molecular phylogenetic analyses are essential in identifying taxonomic units.