The paper presents a mapping tool aiming to identify and minimise potential conflicts between onshore wind energy development and wildlife conservation in Lithuania. It merges current information on the distribution, conservation status and sensitivity of birds and bats to wind power with an integrated evaluation of wind resources (modelled wind speed), special planning status and technical perspectives of wind energy development. The paper includes assessment of the selected wildlife species which were described as sensitive to wind power (69 breeding and 43 migratory bird species and 17 bat species bats in the country). Used species level information allowed the precise identification of sensitive territories and might be used to mitigate negative wind farm effects using special measures based on species behavior. Finally, we delivered overlaps as possible conflicts among the most promising wind farm areas and the areas with high sensitivity in relation to bird and bat distribution. These overlaps point to the required attention and relevant decisions that are needed to ensure sustainable development of wind energy throughout the country. We suggest this tool for initial determination of appropriate areas for wind energy development in the country and as supplement to Environmental Impact Assessment.