According to the National Energy Independence Strategy, Lithuania will aim to reach the target of no less than 23 % of renewable energy in final energy consumption, including no less than 20 % of renewable energy in the electricity sector by 2020. In order to reach this goal, in 2020 Lithuania will have installed wind energy (WE) power plants of 500 MW capacity. At the moment, the development of WE, particularly in the western part of Lithuania, often leads to the conflicts with territories, important to the protection of biodiversity. There is a lack of effective mechanisms for the conflict management, since the actual data on biodiversity, abundance, state of populations of the sensitive to WE development bird and bat species is still poor.