Ectoparasites associated with mountain birds in Costa Rica: linking ecology, biodiversity and genetics
Co-investigator: Ing. Miroslav Čapek, CSc.

Genetic structure of chamois populations in Central Europe (2006-2009)
Investigator: prof. RNDr. Jan Zima, DrSc.

Phylogeography and evolutionary history of a semi-fossorial rodent Microtus subterraneus (2006-2008)
Investigator: Mgr. Natália Martínková, Ph.D.

Species diversity and ecology of selected West African vertebrates
Co-investigator: prof. RNDr. Petr Koubek, CSc.

Diurnal and seasonal patterns of singing activity in Acrocephalus warblers
Investigator: Ing. Miroslav Čapek, CSc.

Comparative phylogeography of Zambezian region in Southeastern Africa using small mammals as a model
Investigator: doc. Mgr. et Mgr. Josef Bryja, Ph.D.

Genetic structure of sika deer populations in the Czech Republic
Investigator: prof. RNDr. Petr Koubek, CSc.

Revision of the species structure of the genera Gobio and Romanogobio in the Eurasian context
Investigator: Mgr. Jan Mendel, Ph.D.

Genetic diversity and phylogeography of the genus Scotophilus
Investigator: Mgr. Peter Vallo, Ph.D.

The ecological importance of set-aside and cultivated crops for the small mammals of agrocenosis
Investigator: Mgr. Eva Jánová, Ph.D.

Intraspecific variability of populations of two cryptic bat species of genus Pipistrellus in Central Europe (2006-2008)
Co-investigator: doc. Mgr. et Mgr. Josef Bryja, Ph.D.

Importance of Red Fox in Different t Ecosystems of Central Europe (2006-2008)
Investigator: prof. Ing. Jaroslav Červený, CSc.

Monitoring of large carnivores in SCI Beskydy
Investigator: prof. RNDr. Petr Koubek, CSc.

Marie Curie intra-European fellowship PHYLOMICROTUS (2006-2008)
Investigator: Mgr. Natália Martínková, Ph.D.

A multidisciplinary study of hybrid zones in the common shrew (2004-2007)
Investigator: prof. RNDr. Jan Zima, DrSc.

Development of new methods of rearing selected promising species for aquaculture using non-traditional technologies (207-2011)
Investigator: Ing. Miroslav Prokeš, CSc.

Development of new technologies of rearing commercially important riverine species of fish and crayfish endangered by environment degradation (2003-2007)
Investigator: Ing. Miroslav Prokeš, CSc.

Biodiversity Research Center (2005-2011)
Co-investigator: prof. RNDr. Jan Zima, DrSc.

The biological and ecological requirements of fishes: factors determining the function of fish ladders
Investigator: doc. ing. Stanislav Lusk, CSc.

Fish biodiversity in the Morava and Dyje confluence area – supporting and stabilization of rare and endangered species populations
Investigator: Ing. Karel Halačka, CSc.

Genetic diversity of endangered fish species-base of effective protection of biodiversity
Investigator: Mgr. Jan Mendel, Ph.D.