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The minute troglobitic species, Zospeum isselianum Pollonera, 1887 (Eupulmonata: Ellobioidea, Carychiidae) is widely distributed within its Southern Alpine-Dinaric range. Its broad distribution and highly variable shell has caused this species to be historically lumped into its current taxonomic state of ambiguity. In an integrative taxonomic approach, phenotypic and genotypic data are synthesized to assess the intraspecific variability recently inferred for this taxon. We collected 16 Zospeum specimens in the Slovenian Alpine Arc encompassing the type locality for Z. isselianum. The material comprises five morphologically recognized (sub)species. The species are re-evaluated using SEM, X-ray nanotomography (nano-CT), conchological, histological and molecular data. Four well-defined lineages are present, which can be attributed to i) Z. isselianum s.str. from its new type locality (Turjeva jama), ii) a highly morphologically variable lineage that so far cannot be attributed to a single morphospecies, iii) Z. kupitzense A. Stummer, 1984 (raised to species rank) and iv) a lineage comprising the two subspecies Z. alpestre alpestre (Freyer, 1855) and Z. alpestre bolei Slapnik, 1991 plus Z. isselianum individuals. The latter is treated as a single taxon Z. alpestre. After considering the severely degraded syntype material of Zospeum isselianum, we provide a taxonomic re-description and propose aneotype for this species. Furthermore, new diagnostic information is revealed regarding the columella of Zospeum isselianum and allied species. Detailed anatomical study reveals new structural aspects of Zospeum morphology and provides groundwork for future investigations.