A molecular (mtDNA and allozyme) data set reveals a clear divergent phylogeny within the Alpine scorpion species Euscorpius (Alpiscorpius) germanus (C. L. Koch, 1837). Two distinct (ca. 7 % DNA sequence divergence), monophyletic clades exist which are geographically separated by the Adige (Etsch) River in northern Italy. At the allozyme level, these population groups are fixed for alternative alleles at eight out of 18 gene loci and correspond roughly to the morphological subspecies E. g. germanus and E. g. alpha. No evidence of introgressive hybridization between the two groups is shown by the allozyme data. The branching points of the two population groups are found at unusually high distances compared with the outgroup taxa E. gamma Caporiacco, 1950 and E. flavicaudis (De Geer, 1778). The subspecies E. g. alpha is therefore elevated to species level: Euscorpius alpha Caporiacco, 1950, stat, nov. A neotype for E. germanus (C. L. Koch, 1837) and lectotypes for E. alpha stat. nov., E. germanus beta syn, nov. of E. alpha, and E. germanus croaticus are designated. Phylogenetic and biogeographic implications are discussed.