The timely and effective establishment of Natura 2000 network is one of the greatest environmental challenges for the new Member States of the European Union. Slovak Republic is facing this challenge now. By the June 2005, the Government in our country must prepare a list of sites to be included in the Natura network, according to the criteria set up in the Habitat Directive. Natura 2000 sites, according to the specificEUDirectivesconsistofSpecialAreasofConservation(SACs),andSpecialProtectionAreas(SPAs).TheSPAsandtheSACs, the latter selected as Sites of Community Importance (SCIs), will be incorporated into the Natura 2000 network. The problems of proclaiming the system of protected areas of European importance for the Natura 2000 have been one of the major topics of the ichthyological activities in our country in recent years. For 3 lampreys and 20 fishspeciestheterritoryofpotentialsiteofcommunityinterest(pSCI)hasbeenlimitedandproposed.Theselection of localities and examinations of population state in individual species of fishespresentedintheAnnex(II.,IVandV.)totheCouncilDirective No. 92/43/EEC were carried out in 2003/2004. In total 179 pSCI localities for fishandlampreysinthealpinebiogeographicregion (83) and in the pannonian biogeographic region (96) pSCI in the Slovak republic were selected and limited. The number of pSCI localities selected for individual species is different regards to their distribution within the river net of Slovakia. For example, for species of general distribution, 30 localities pSCI (Misgurnus fossilis, Rhodeus sericeus, Gobio albipinnatus, Barbus barbus) or 35 localities pSCI (Cobitis elongatoides, Barbus peloponnesius), have been proposed, on the contrary, in several species of exclusive distribution as Lampetra planeri - 8, Gobio uranoscopus - 9 and Zingel zingel -12 localities. The pSCI territory for individual species of the ichthyofauna presented here represents the firststageintheprocessofcreatingtheprotected territory system of European interest Natura 2000 in the territory of the Slovakia for this group of aquatic vertebrates. The list of proposal sites will have to be submitted to the European Commission by the date of Accession.