Abstract The beetle subtribe Anthroherponina (Coleoptera: Leiodidae), including also ecologically specialized and semi-aquatic hygropetricolous genera, presents one of the most illustrative examples of morphological variability in cave-adapted animals. However, phylogenetic relations within the tribe remain dubious. Recent exploration of deep-phreatic caves of the Western Balkans Dinaric Karst enabled us to collect all known Anthroherponina genera and access new populations of hygropetricolous beetles, representatives of the iconic Hadesia and elusive Nauticiella. We studied the taxonomic structure of newly collected semi-aquatic beetle populations by using traditional morphology and deploying uni- and multilocus molecular species delimitation. In addition, we tested the monophyly of the subtribe Anthroherponina and set the group’s evolutionary development into a palaeogeographic context by reconstructing a multilocus calibrated phylogeny. As a result, three new species of specialized semi-aquatic beetles are described. The morphologically based monophyly of Anthroherponina was shown to be an artefact of evolutionary convergences, while the evolutionary development of the monophylum seems to be paired with the orogeny of the Dinarides. Finally, the new results raise more questions about our understanding of evolution in subterranean beetles and their adaptation to special ecological niches.