Lajbner Z, Linhart O, Kotlík P (2011) Human-aided dispersal has altered but not erased the phylogeography of the tench. Evolutionary Applications, doi: 10.1111/j.1752-4571.2010.00174.x  

Lajbner Z., Kotlík P. (2011) PCR-RFLP assays to distinguish the Western and Eastern phylogroups in wild and cultured tench Tinca tinca. Molecular Ecology Resources, doi: 10.1111/j.1755-0998.2010.02914.x

Musilová R, Zavadil V, Marková S, Kotlík P (2010) Relics of the Europe's warm past: Phylogeography of the Aesculapian snake. Molecular Phylogenetics and Evolution, 57, 1245-1252.  

Lajbner Z, Kohlmann K, Linhart O, Kotlík P (2010) Lack of reproductive isolation between the Western and Eastern phylogroups of the tench. Reviews in Fish Biology and Fisheries, 20, 289-300.  

Gvoždík V, Moravec J, Klutsch C, Kotlík P (2010) Phylogeography of the Middle Eastern tree frogs (Hyla, Hylidae, Amphibia) as inferred from nuclear and mitochondrial DNA variation, with a description of a new species. Molecular Phylogenetics and Evolution, 55, 1146-1166.  

Marková S, Šanda R, Crivelli A, Shumka S, Wilson IF, Vukić J, Berrebi P, Kotlík P (2010) Nuclear and mitochondrial DNA sequence data reveal the evolutionary history of Barbus (Cyprinidae) in the ancient lake systems of the Balkans. Molecular Phylogenetics and Evolution, 55, 488-500.  

Wójcik JM, Kawałko A, Marková S, Searle JB, Kotlík P (2010) Phylogeographic signatures of post-glacial colonization from high-latitude refugia: a case study of bank voles using museum specimens. Journal of Zoology, 281, 249-262.  

Searle JB, Kotlík P, Rambau RV, Marková S, Herman JS, McDevitt AD (2009) The Celtic fringe of Britain: insights from small mammal phylogeography. Proceedings of the Royal Society of London. B - Biological Sciences, 276, 4287-4294.  

Kotlík P, Marková S, Choleva L, Bogutskaya NG, Ekmekci FG, Ivanova PP (2008) Divergence with gene flow between Ponto-Caspian refugia in an anadromous cyprinid Rutilus frisii revealed by multiple gene phylogeography. Molecular Ecology, 17, 1076-1088.  

Marková S, Dufresne F, Rees DJ, Černý M, Kotlík P (2007) Cryptic intercontinental colonization in water fleas Daphnia pulicaria inferred from phylogenetic analysis of mitochondrial DNA variation. Molecular Phylogenetics and Evolution, 44, 42-52.  

Kotlík P, Deffontaine V, Mascheretti S, Zima J, Michaux JR, Searle JB (2006) A northern glacial refugium for bank voles (Clethrionomys glareolus). Proceedings of the National Academy of Sciences of the United States of America (PNAS), 103, 14860-14864.  

Janko K, Culling MA, Ráb P, Kotlík P (2005) Ice age cloning - comparison of the Quaternary evolutionary histories of sexual and clonal forms of spiny loaches (Cobitis : Teleostei) using the analysis of mitochondrial DNA variation. Molecular Ecology, 14, 2991-3004.  

Kotlík, P, Bogutskaya NG, Ekmekçi FG (2004) Circum Black Sea phylogeography of Barbus freshwater fishes: divergence in the Pontic glacial refugium. Molecular Ecology, 13, 87-95.  

Kotlík P, Tsigenopoulos CS, Ráb P, Berrebi, P. (2002) Two new Barbus species from the Danube River basin, with redescription of B. petenyi (Teleostei: Cyprinidae) Folia Zoologica, 51, 227-240.  

Kotlík P, Berrebi P (2002) Genetic subdivision and biogeography of the Danubian rheophilic barb Barbus petenyi inferred from phylogenetic analysis of mitochondrial DNA variation. Molecular Phylogenetics and Evolution, 24, 10-18.  

Kotlík P, Berrebi P (2001) Phylogeography of the barbel (Barbus barbus) assessed by mitochondrial DNA variation. Molecular Ecology, 10, 2177-2186.