Background The strategic goal of Croatia’s nature protection policy was to satisfy the preconditions to fulfil its international and European commitments. Special attention had to be given to the requirements related to the EU Habitats and Birds Directives. Furthermore, in 2001, Croatia was invited by Visegrad group (Hungary, the Czech Republic, Slovakia and Poland) to participate, together with Ukraine (the so-called Visegrad 4+2 group of countries), in a project to develop a map of regional ecological networks for the six countries. Objectives The project’s overall objective was to contribute to the implementation of EU nature protection policy and legislation in Croatia. Specifically, the project aimed to strengthen the capacity of the national nature protection authority to fulfil Croatia’s international commitments as a country in the process of accession to the EU, identify areas that would become part of the Natura 2000 and National Ecological networks, build up the National Ecological Network (NEN) as a coherent part of the Pan-European Ecological Network and the Regional Ecological Network of the Visegrad 4+2 countries, and develop a network of people involved in data gathering for nature conservation. Results The project trained nature protection authorities, developed a map of National ecological network and set up a network of associates involved in gathering data on biological diversity as a basis for the National Biodiversity Monitoring System. Special attention was given to the requirements related to the EU Habitats and Bird Directives, which aim to identify and designate sites important for maintaining or even restoring threatened habitats and species in a favourable conservation status. Such sites, identified and documented through the Natura 2000 programme, create the basis for the Pan-European Ecological Network (PEEN). Croatia had to contribute to the PEEN by creating its own national ecological network, a demand that was fulfilled by the CRO-NEN project. The network consists of international and national ecologically important areas connected by corridors, ensuring the long-term survival of threatened habitats and species. The core activity of the project was to collect, to structure and digitise the missing information with respect to the requirements of the above mentioned EU directives. The beneficiary prepared distribution maps of threatened species in Croatia. The main data source was the red list of threatened species in Croatia, with the SINP summarising lists of bird species and habitats occurring in Croatia according to the respective EU Directives. The data was then entered in the newly developed CRO-NEN database. The beneficiary was able to use existing sources, but at the same time, the State Institute of Nature Protection (SINP) and contracted experts had to work hard to gather up-to-date information. The project also developed a related a GIS system and new software that was compatible with that of Natura 2000.