Numerous changes in biosphere of mainly anthropogenic origin have given rise to the loss of biodiversity. Therefore, it becomes increasingly more important to develop the progressive and effective methods for the biodiversity research and monitoring. Establishing of network of sites with appropriate design for the long-term monitoring research of biodiversity must follow several methodical and integrative factors. Developing and knowledge of biodiversity indicators and surrogates as well as communication between scientists, public and policy makers can provide suitable base for implementation of as much as possible aspects for the biodiversity assessment. Establishment of viable Network of Excellence (NoE) will create European long-term inter-disciplinary facility for research on the complex relationship between ecosystems, biodiversity and society. This contribution brings together the most important information and partial results related to one of the main biodiversity aimed projects running under the Framework Programme 6: A Longterm Biodiversity, Ecosystem and Awareness Research Network (ALTER-Net). 24 European organisations has been participated within the frame of this project, Slovakia is represented by the Institute of Landscape Ecology Slovak Academy of Sciences. Participating at the project ALTER-Net tasks contributes essentially to understanding and better awareness of the biodiversity problems and helps to develop communication and partnership between scientists, policy makers and public.