Freyhof, J., Lieckfeldt, D., Pitra, C. & Ludwig A. 2005. Molecules and morphology: evidence for introgression of mitochondrial DNA in Dalmatian cyprinids. Molecular Phylogenetics and Evolution, 37: 347-354. (4.213)
  Nolte, A., Freyhof, J., Stemshorn, K. & Tautz, D. 2005. An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated by hybridization between old phylogeographic groups. Proceedings of the Royal Society, London, 272: 2379-2387. (3.653)
  Freyhof, J. & Korte, E., 2005. The first record of Misgurnus anguillicaudatus in Germany. Journal of Fish Biology, 66: 568-571. (1.198)
  Freyhof, J. & Kottelat, M. 2005. Salvelinus evasus sp. n., a charr from deep waters of Lake Ammersee, southern Germany (Teleostei: Salmonidae), with comments on two extinct species. Revue Suisse de Zoologie, 112: 253-269. (0.284)
  Bohlen, Freyhof, J. & Wolter, C. 2005. First records of Cobitis elongatoides and Sabanejewia baltica (Cobitidae) for Germany. Cybium, 29: 103-104. (0.312)
  Freyhof, J. 2005. Redescription of Coregonus bavaricus Hofer, 1909, an endemic species to Lake Ammersee, Germany (Salmoniformes: Coregonidae). Cybium, 29: 179-183. (0.312)
  Freyhof, J., Kottelat, M. & Nolte, A. 2005. Taxonomic diversity of European Cottus with description of eight new species (Teleostei: Cottidae). Ichthyological Exploration of Freshwaters, 16: 107-172.
  Freyhof, J. & Schöter, C. 2005. The Houting, Coregonus oxyrinchus (L.), a globally extinct species from the North Sea basin (Salmoniformes: Coregonidae). Journal of Fish Biology, 67: 713-729. (1.198)
  Copp, G.H., Bianco, P.G., Bogutskaya, N.G., Erős, T., Falka, I., Ferreira, M.T., Fox, M.G., Freyhof, J., Gozlan, R.E., Grabowska, J., Kováč, V., Moreno-Amich, R., Naseka, A.M., Peňáz, M., Povž, M., Przybylski, M., Robillard, M., Russell, I.C., Stakėnas, S., Šumer, S., Vila-Gispert, A. & Wieser, C. 2005. To be, or not to be, a non-native freshwater fish. Journal of Applied Ichthyology, 21: 242-262. (0.478)
  Ng, H. H. & Freyhof, J. 2005. Pseudomystus sobrinus a new catfish (Teleostei: Bagridae) from central Vietnam. Copeia, 744-749. (0.824)
  Naseka A. M., Spodareva V. V., Freyhof J., Bogutskaya N. G., Poznjak V. G. 2005. New data to species composition and distribution of gudgeons (Gobioninae, Cyprinidae, Teleostei) in River Kuban. Folia Zoologica, 54, Suppl.: 50-55. (0.536)
  Freyhof, J. & Naseka, A. M. 2005. Gobio delyamurei, a new gudgeon from Crimean Peninsular (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 16, 331-338.