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.