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.


  Nolte, A. W., Freyhof, J., & Tautz, D. 2006. When invaders meet locally adapted types: rapid moulding of hybrid zones between two species of sculpins (Cottus, Pisces). Molecular Ecology, 15: 1983-1989. (4.301) .
  Freyhof, J., Lieckfeldt, D., Bogutskaya, N. G. & Ludwig A. 2006. Phylogenetic position of the Dalmatian genus Phoxinellus and description of Delminichthys, new genus, (Teleostei: Cyprinidae). Molecular Phylogenetics and Evolution, 38: 416-425. (3.431)
  Šlechtová, V., Bohlen, J., Freyhof, J. & Rab, P. 2006. Molecular phylogeny of the Southeast Asian freshwater fish family Botiidae (Teleostei: Cobitoidea) and the origin of polyploidisation in their evolution. Molecular Phylogenetics and Evolution, 39: 529-541. (3.431)
  Bohlen, J., Slechtova, V., Bogutskaya, N. G. & Freyhof, J. 2006. Across Siberia and over Europe: Phylogenetic relationships of the freshwater fish genus Rhodeus in Europe and the phylogenetic position of R. sericeus from the River Amur. Molecular Phylogenetics and Evolution, 40: 856-865. (3.431)
  Schulz, M., Freyhof, J., Saint-Laurent, R., Østbye, K., Mehner, T. & Bernatchez, L. 2006. Evidence for independent origin of two spring-spawning ciscoes in Germany (Salmoniformes: Coregonidae). Journal of Fish Biology 68, Suppl. A: 119-135. (1.188)
  Herder, F. & Freyhof, J. 2006. Niche differentiation of fishes in a medium-sized tropical stream. Journal of Fish Biology, 68: 571-589 (1.188)
  Yang, J., He, S., Freyhof, J., Witte, K.-E. & Liu, H. 2006. Phylogeny of the Gobioninae inferred from complete mitochondrial cytochrome b gene sequences (Teleostei: Cyprinidae). Hydrobiologia, 553: 255-266. (0.978)
  Sindilariu, P. D., Freyhof, J. & Wolter, C. 2006. Habitat use of juvenile fish in the lower Danube and the Danube Delta: implications for ecotone connectivity. Hydrobiologia, 571: 51-61. (0.978)
  Freyhof; J. & Özuluğ, M. 2006. Pseudophoxinus ninae, a new species from Central Anatolia, Turkey (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 17: 255-259.


  Kottelat, M. & Freyhof, J. 2007. Handbook of European freshwater fishes. Kottelat, Cornol and Freyhof, Berlin, xiv + 646 pp.
  Helland, I. P., Freyhof, J., Kasprzak, P. & Mehner, T. 2007. Temperature sensitivity of vertical distributions of zooplankton and planktivorous fish in a stratified lake. Oecologia, 151. 322-330. (3.333)
  Mayden, R. L., Tang, K. L., Conway, K. W., Freyhof, J., Chamberlain, S., Haskins, M., Schneider, L., Sudkamp, M., Wood, R. M., Agnew, M., Bufalino, A., Sulaiman, Z., Miya, M., Saitoh, K. & He, S.-H. 2007. Phylogenetic relationship of Danio within the order Cypriniformes: A framework for comparative and evolutionary studies of a model species. Journal of Experimental Zoology, 308B: 642-654. (2.756)
  Ng, H. H. & Freyhof, J. 2007. Pseudobagrus nubilosus, a new species of catfish from central Vietnam (Teleostei: Bagridae), with notes on the validities of Pelteobagrus and Pseudobagrus. Ichthyological Exploration of Freshwaters, 18: 9-16.
  Kottelat, M. & Freyhof, J. 2007. Pelasgus, a new genus name for the Balkan species of Pseudophoxinus (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 18: 103-108.
  Freyhof, J., & Kottelat, M. 2007. Alburnus vistonicus, a new shemaya from eastern Greece, with remarks on Chalcalburnus chalcoides macedonicus from Lake Volvi (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 18: 205-212.
  Freyhof, J., & Kottelat, M. 2007. Review of the Alburnus mento species group with description of two new species (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 18: 213-225.
  Özuluğ, M. & Freyhof, J. 2007. Rediagnosis of four shemajas from western Turkey and description of two new species (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 18: 233-246.
  Freyhof, J. & Stelbrink, B. 2007. Cobitis illyrica, a new species of loach from Adriatic basin, Croatia (Teleostei: Cobitidae). Ichthyological Exploration of Freshwaters, 18: 269-275.
  Özuluğ, M. & Freyhof; J. 2007. Alburnus demiri, a new species of bleak from Western Anatolia, Turkey (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 18: 307-312.
  Freyhof, J. & Naseka, A. M. 2007. Proterorhinus tataricus, a new tubenose goby from Crimea, Ukraine (Teleostei: Gobiidae). Ichthyological Exploration of Freshwaters, 18: 325-334.


  Cano, J. M., Mäkinen, H. S, Leinonen, T, Freyhof, J. & Merilä, J. 2008. Extreme neutral genetic and morphological divergence supports Adriatic threespined stickleback (Gasterosteus aculeatus) populations as conservation units. Biological Conservation, 141: 1055-1066. (3.296)
  Helland, I. P., Harrod, C., Freyhof, J. & Mehner, T. 2008. Coexistence of a pair of pelagic planktivorous coregonid fish. Evolutionary Ecology Research, 10: 373-390. (1.404)
  Tang, Q, Freyhof, J, Xiong, B, & Liu, H. 2008. Multiple invasions of Europe by East Asian cobitid loaches (Teleostei: Cobitidae). Hydrobiologia, 605: 17-28. (1.201)
  Ng, H. H. & Freyhof, J. 2008. Two new species of Glyptothorax (Teleostei: Sisoridae) from Central Vietnam. Zootaxa, 1873: 11-25. (0.691)
  Özuluğ, M. & Freyhof; J. 2008. Capoeta turani, a new species of barbel from River Seyhan, Turkey (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 19: 289-296. (0.730)
  Freyhof, J., Stelbrink, B., Özuluğ, M. & Economidis. P. S. 2008. The first record of Cobitis puncticulata from Europe with comments on its conservation status (Teleostei: Cobitidae). Folia Zoologica, 57: 16-19. (0.376)
  Bohlen, J., Freyhof, J. & Nolte, A. 2008. Sex ratio and body size in Cobitis elongatoides and Sabanejewia balcanica (Cypriniformes; Cobitidae) from a thermal spring. Folia Zoologica, 57: 191-197. (0.376)


  Mehner, T., Pohlmann, K., Elkin, C., Monaghan, M. & Freyhof, J. 2009. Genetic mixing from enhancement stocking in commercially exploited vendace populations. Journal of Applied Ecology, 46: 1340-1349. (4.220)
  Almada, V. C., Robalo, J. I., Levy, A., Freyhof, J., Bernardi, G., & Doadrio, I. 2009. Phylogenetic analysis of Peri-Mediterranean blennies of the genus Salaria: molecular insight on the colonization of freshwaters. Molecular Phylogenetics and Evolution, 52: 424-431. (3.994)
  Larmuseau, M. H. D., Freyhof, J., Volckaert, F. A. M. & Van Houdt, J. K. J. 2009. Matrilinear phylogeography and demographical patterns of the freshwater fish Rutilus rutilus: implications for taxonomy and conservation. Journal of Fish Biology, 75: 332-253. (1.404)
  Helland, I. P., Vollestad, L. A., Freyhof, J. & Mehner, T. 2009. Morphological differences between two ecologically similar sympatric fish species. Journal of Fish Biology, 75, 2756-2767. (1.404)
  Kottelat, M. & Freyhof, J. 2009. Notes on the taxonomy and nomenclature of some European freshwater fishes. Ichthyological Exploration of Freshwaters, 20: 75-90. (0.754)
  Schöter, C., Özuluğ, M. & Freyhof, J. 2009. Capoeta caelestis, a new species from River Göksu, Turkey (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 20: 229-236. (0.754)
  Freyhof, J. 2009. Rote Liste der im Süßwasser reproduzierenden Neunaugen und Fische (Cyclostomata & Pisces), fünfte Fassung. Naturschutz und Biologische Vielfalt, 70: 291-316.
  Freyhof; J. & Özuluğ, M. 2009. Pseudophoxinus fahrettini, a new species of spring minnow from Central Anatolia (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 20: 339-346. (0.754)
  Freyhof; J. & Özuluğ, M. 2009. Pseudophoxinus evliyae, a new species of spring minnow from Western Anatolia with remarks on the distribution of P. ninae and the systematic position of P. fahirae (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 20: 347-356. (0.754)
  Lang, N. J., Roe, K. J., Renaud, C. B., Gill, H. S., Potter, I. C., Freyhof, J., Naseka, A., Cochran, P., Pérez, H. E., Habit, E. M., Kuhajda, B. R., Lyons, J., Neely, D. A., Reshtnikov, Y., Salnikov, V., Stoumboudi, M. T. & Mayden, R. L. 2009. Novel relationships among lampreys (Petromyzontiformes) revealed by a taxonomically comprehensive dataset. American Fisheries Society Symposiums, 72: 41-55.
  Borkenhagen, K. & Freyhof, J. 2009. New records of the Levantine endemic cichlid Tristramella simonis (Günther, 1864) from Syria. Cybium, 33: 335-336. (0.541)