Acanthocephalans are obligate parasites of vertebrates, mostly of fish. There is limited knowledge about the diversity of fish-parasitizing Acanthocephala in Austria. Seven determined species and an undetermined species are recorded for Austrian waters. Morphological identification of acanthocephalans remains challenging due to their sparse morphological characters and their high intraspecific variations. DNA barcoding is an effective tool for taxonomic assignment at the species level. In this study, we provide new DNA barcoding data for three genera of Acanthocephala (Pomphorhynchus Monticelli, 1905, Echinorhynchus Zoega in Müller, 1776 and Acanthocephalus Koelreuter, 1771) obtained from different fish species in Austria and provide an important contribution to acanthocephalan taxonomy and distribution in Austrian fish. Nevertheless, the taxonomic assignment of one species must remain open. We found indications for cryptic species within Echinorhynchus cinctulus Porta, 1905. Our study underlines the difficulties in processing reliable DNA barcodes and highlights the importance of the establishment of such DNA barcodes to overcome these. To achieve this goal, it is necessary to collect and compare material across Europe allowing a comprehensive revision of the phylum in Europe.

New biological species and high levels of inter- and intraspecific genetic divergence were discovered in an allozyme study of some North European members of the acanthocephalan genus Echinorhynchus (sensu lato), parasites of fish and malacostracan crustaceans. (i) A strong differentiation between the marine E. gadi and the fresh- and brackish-water E. salmonis (genetic identity I ≃ 0) supports a generic distinction between these taxa; however, the subdivision would not entirely concur with the concepts of Echinorhynchus (sensu stricto) and Metechinorhynchus suggested earlier. (ii) Samples of E. gadi from the Baltic, Norwegian and North Seas included three distinct, partially sympatric biological species (spp. I–III; I ≃ 0·5). (iii) E. bothniensis, previously only known from the northern Baltic Sea, represents a complex of freshwater taxa with an intermediate host relationship to the ‘glacial relict’ Mysis spp. and with a distributional and host analogy to the North American E. leidyi. A population in a northern lake in the Barents Sea basin is closely related to E. bothniensis of the Baltic area, but is probably specifically distinct; the divergence between these populations (I ≃ 0·6) is similar to that between their Mysis host species. (iv) Considerable intraspecific differentiation (Fst = 0·25), probably reflecting post-glacial population bottlenecks, was found between Baltic and nearby lacustrine E. bothniensis, and between Atlantic and Baltic E. gadi sp. I.