Protected areas play a significant role in the conservation of ecosystem biodiversity and natural state. Establishing the status of given animal and plant species and their habitat hints to the urgent need to ensure special protection of certain areas and their declaration as protected sites, both at national and cross-border level. So far within the national framework initial steps have been taken to identify Natura 2000 sites at national level, but we believe that much more work still remains ahead. We also hope and strive to implement the concept of ecological networks. The programme for management of protected areas aims at monitoring of and taking active participation into the process to upgrade the system of protected areas in Macedonia. As part of this programme we seek successful sharing of information in order to improve the protected area status, particularly by providing training, consultation and concrete actions. In that respect, MES makes continuous contribution for better planning and management of protected areas, and promotes the concept of area conservation as basis to ensure conditions needed for biodiversity protection and to include the locals’ needs and benefits, and the resources, as a novel concept of nature protection.