At present the genus Alpioniscus includes two subgenera: Alpioniscus s. str. and Illyrionethes. The latter includes 13 species in the Dinaric Karst, two species from Sardinia (A. fragilis (Budde-Lund, 1885) and A. thanit Taiti & Argano, 2009) and one from Spain (A. escolai Cruz & Dalens, 1989). All known species of the genus Alpioniscus are troglobiotic except for the Sardinian endogean species A. thanit. A total of 3763 specimens of Illyrionethes were found in 308 caves from the Dinaric Karst. Molecular analyses were conducted on 35 different populations from 52 caves (1-4 specimens for each population), using two mtDNA genes (16S rRNA and COXI) and a nuclear one (H3). On the basis of morphological analyses two different groups were identified, while by molecular analyses some distinct groups are recognized, each with a merodinaric distribution. The strasseri group consists of six subgroups, and has a northwestern Dinaric distribution. Four groups have a southeastern distribution pattern: two monotypic groups (absoloni and verhoeffi) and two groups (heroldi and herzegowinensis) each consisting of two subgroups. Two groups (magnus and haasi) include four subgroups and have a paralittoral distribution. The strasseri, absoloni, veroheoffi, and heroldi groups are well characterized both morphologically and molecularly, the haasi and herzegowinensis groups are morphologically the most diversified each other, and magnus group is morphologically not well supported. Some groups are geographically overlapping: on the Biokovo Mt. three different groups (strasseri, heroldi and verhoeffi) are present. Syntopic species are relatively rare, more than two species together were never reported. The distribution pattern of Illyrionethes phylogroups seems to be different from that of phylogroups of other cave dwelling fauna in the Dinaric Karst