2001

• Zrzavý, J.; Hypša, V.; Tietz, D.F. 2001: Myzostomida are not annelids: molecular and morphological support for a clade of animals with anterior sperm flagella. Cladistics, 17: 170–198. DOI: 10.1111/j.1096-0031.2001.tb00116.x

2002

• Zrzavý, J. 2002: Gastrotricha and metazoan phylogeny. Zoologica scripta, 32: 61–81. DOI: 10.1046/j.1463-6409.2003.00104.x

2004

• Fric, Z., Konvicka, M. & Zrzavý, J. 2004. Red & black or black & white? Phylogeny of the Araschnia butterflies (Lepidoptera: Nymphalidae) and evolution of seasonal polyphenism. Journal of Evolutionary Biology 17(2): 265–278. DOI: 10.1111/j.1420-9101.2003.00681.x . Reference page. 

• Pech, P., Fric, Z., Konvicka, M. & Zrzavý, J. 2004. Phylogeny of Maculinea blues (Lepidoptera: Lycaenidae) based on morphological and ecological characters: evolution of parasitic myrmecophily. Cladistics 20(4): 362–375. DOI: 10.1111/j.1096-0031.2004.00031.x . Reference page. 

2007

• Fric, Z., Wahlberg, N., Pech, P. & Zrzavý, J. 2007. Phylogeny and classification of the Phengaris–Maculinea clade (Lepidoptera: Lycaenidae): total evidence and phylogenetic species concepts. Systematic entomology 32: 558–567. DOI: 10.1111/j.1365-3113.2007.00387.x Reference page. 

2008

• Zrzavý, J. 2008. Four chapters about the monophyly of insect 'orders': a review of recent phylogenetic contributions. Acta Entomologica Musei Nationalis Pragae 48(2): 217–232. PDF Reference page. 

2009

• Zrzavý, J. et al. 2009: Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes. BMC evolutionary biology, 9: 189. DOI: 10.1186/1471-2148-9-189