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2000

  Englbrecht, C., Freyhof, J., Nolte, A., Rassmann, K., Schliewen, U. & Tautz, D. 2000. Phylogeography of the bullhead Cottus gobio (Pisces: Teleostei: Cottidae) suggests a pre-Pleistocene origin of the major Central European populations. Molecular Ecology, 9: 709-722. (5.560)
  Freyhof, J., Scholten, M., Bischoff, A., Wanzenböck, J., Staas, S. & Wolter, C., 2000. Extensions to the known range of the whitefin gudgeon Gobio albipinnatus Lukasch, 1933, in Europe and biogeographical implications. Journal of Fish Biology, 57: 1339-1342. (1.195)
  Freyhof, J. A. & Serov, D. V. 2000. Cobitis laoensis (Sauvage, 1878) from Vietnam with notes on the southern distribution limits of Indochinese Cobitis. Folia Zoologica, 49 (Suppl. 1): 205-214. (0.655)
  Freyhof, J., Ráb, P., & Bohlen, J. 2000. The valid names of some European species of the genus Cobitis (Teleostei, Cobitidae). Folia Zoologica, 49 (Suppl. 1), 3-7. (0.655)
  Freyhof, J. & Serov, D. V. 2000. Review of the genus Sewellia from Vietnam with descriptions of two new species (Cypriniformes: Balitoridae). Ichthyological Exploration of Freshwaters, 11: 217-240.

2001

  Vences, M., Freyhof, J., Sonnenberg, R., Kosuch, J. & Veith, M. 2001. Reconciling fossils and molecules? Possible Cenozoic divergence of cichlid fishes, and the biogeography of Madagascar. Journal of Biogeography, 28: 1091-1100. (4.087)
  Ng, H. H. & Freyhof, J. 2001. A review of the catfish genus Pterocryptis (Siluridae) in Vietnam, with the description of two new species Journal of Fish Biology, 59: 624-644. (1.195)
  Ng, H. H. & Freyhof, J. 2001. Oreoglanis infulatus, a new species of glyptosternine catfish (Siluriformes: Sisoridae) from central Vietnam. Journal of Fish Biology, 59: 1164-1169. (1.195)
  Freyhof, J. & Serov, D. V. 2001. Nemacheiline loaches from Central Vietnam with descriptions of a new genus and 14 new species (Cypriniformes: Balitoridae). Ichthyological Exploration of Freshwaters, 12: 133-191.
  Freyhof, J. & Herder, F. 2001. Tanichthys micagemmae, a new miniature cyprinid fish from Central Vietnam (Cypriniformes: Cyprinidae). Ichthyological Exploration of Freshwaters, 12: 215-220.

2002

  Freyhof, J. 2002. Freshwater fish diversity in Germany, threats and species extinction, pp. 3-22. In: Collares-Pereira, M. J., Coelho, M. M. & Cowx, I. G. Freshwater fish conservation: options for the future, Blackwell Publishers 462 pp.
  Bohlen, J., Rab, P., Slechtova, V., Rabova, M., Ritterbusch, D., & Freyhof, J. 2002. Hybridogenous biotypes in spined loaches (genus Cobitis) in Germany with implications for conservation, pp. 311-321. In: Collares-Pereira, M. J., Coelho, M. M. & Cowx, I. G. Freshwater fish conservation: options for the future, Blackwell Publishers, 462 pp.
  Freyhof, J. & Herder, F. 2002 Records of genus Hemimyzon in Vietnam, with the description of a new species (Cypriniformes: Balitoridae). Ichthyological Exploration of Freshwaters, 13: 53-58.
  Freyhof, J. & Herder, F. 2002. Review of the paradise fishes of the genus Macropodus in Vietnam, with description of two new species from Vietnam and southern China (Perciformes: Osphronemidae). Ichthyological Exploration of Freshwaters, 13: 147-167.
  Sindilariu, P. D., Bacalbasa-Dobrovici, N., Freyhof, J., & Wolter, C., 2002. The juvenile fish community of the lower Danube and the Danube Delta. International Association for Danube Research, 34: 517-526.

2003

  Schulz, M. & Freyhof, J. 2003. Coregonus fontanae, a new spring-spawning cisco from Lake Stechlin, northern Germany (Salmoniformes: Coregonidae). Ichthyological Exploration of Freshwaters, 14: 209-214.
  Freyhof, J. 2003. Sewellia albisuera, a new balitorid loach from Central Vietnam (Cypriniformes: Balitoridae). Ichthyological Exploration of Freshwaters, 14: 225-230.
  Ng, H. H. & Freyhof, J. 2003. Akysis clavulus, a new species of catfish (Teleostei: Akysidae) from Central Vietnam. Ichthyological Exploration of Freshwaters, 14: 311-316.
  Sindilariu, P. D. & Freyhof, J. 2003. Food overlap of benthic fishes in the Danube Delta, with special respect to two invasive gobiids (Teleostei: Gobiidae, Percidae, Cyprinidae). Lauterbornia, 46: 149-157.
  Freyhof, J. 2003. Immigration and potential impacts of invasive freshwater fishes in Germany. Berichte des IGB, 17: 51-58.

2004

  Šlechtová, V., Bohlen, J., Freyhof, J., Persat, H., & Delmastro, G. 2004. The Alps as barrier to dispersal in cold-adapted freshwater fishes? Phylogeographic history and taxonomic state of the bullhead in the Adriatic freshwater drainage. Molecular Phylogenetics and Evolution, 33: 225-239. (4.213)
  Wolter, C. & Freyhof, J. 2004. Diel fish movements in a temperate large lowland river. Journal of Fish Biology, 64: 632-642. (1.198)
  Freyhof, J. & Brunken, H. 2004. Erste Einschätzung der Verantwortlichkeit Deutschlands für die Erhaltung von Fischarten und Neunaugen des Süßwassers. Naturschutz und Biologische Vielfalt, 8: 133-144.
  Naseka, A. M. & Freyhof, J. 2004. Romanogobio parvus, a new gudgeon from River Kuban, southern Russia (Cyprinidae, Gobioninae). Ichthyological Exploration of Freshwaters, 15: 17-23.
  Bogutskaya, N. G., Movchan, Y. V. & Freyhof, J. 2004. On Barbus waleckii Rolik, 1970 (Cyprinidae) in Ukraine with brief remarks on species from the genus Barbus Cuvier, 1816, distributed in the Dniestr and Vistula drainages. Vestnik Zoologii, Kiev, 38: 87-92.
  Freyhof, J. & Herder, F. 2004. Comments on the proposed conservation of the specific name of M. concolor Ahl, 1937 (Osteichthyes, Perciformes). Bulletin of Zoological Nomenclature, 61 (3): 173-174.

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