Species of the genus Pomphorhynchus Monticelli, 1905 (Acanthocephala: Pomphorhynchidae) are obligate endoparasites infesting mostly freshwater fish. Morphological identification is challenging due to high intraspecific variations. The use of molecular analyses enabled new insights into the diversity and revealed high cryptic presence and unknown distribution patterns for various European species. In Austria only one species, Pomphorhynchus laevis (Müller, 1776), has been reported so far. We conduct an integrative analysis of Pomphorhynchus in Austria with a combination of morphological and molecular methods. Our results revealed the presence of three species of Pomphorhynchus in Austrian waters: Pomphorhynchus laevis, Pomphorhynchus tereticollis (Rudolphi, 1809) and Pomphorhynchus bosniacus Kiskároly and Čanković, 1967. While P. bosniacus was the predominant species in the Danube, P. laevis was recorded exclusively in Styria. Pomphorhynchus tereticollis occurred mainly in rivers of Styria except for one individual found in the Danube. We document the first occurrence of P. bosniacus and P. tereticollis in Austria. We found a high intraspecific haplotype variation in P. bosniacus suggesting that the species has a longer history in Central and Western Europe. It was previously misidentified as P. laevis, which is also true for P. tereticollis. A large number of hosts examined were infected with only juvenile and cystacanth stages suggesting paratenic infections. Our study highlights the importance of using an integrative taxonomic approach in the identification of species of Pomphorhynchus. Keywords: Acanthocephala, Pomphorhynchus spp., Austria, Fish, Autofluorescence imaging, Integrative taxonomy, 3-D reconstructio