This report provides an overview and future challenges of animal, plant, and ecosystem impact assessments in the Environmental Impact Assessment Act. Red List species, subject to animal and plant impact assessments, generally have a small population, and field surveys often do not provide sufficient data. Therefore, species-specific information, especially habitat data, is essential for impact assessment. Ecosystem impact assessments have been conducted using regional indicator species. However, planning stage procedures introduced by law revision focus on a rather critical natural environment. In addition, international organizations recently applied red list assessments to plant communities, habitats, and ecosystems. In the future, the red list of ecosystems will be beneficial for assessing impacts on the Japanese natural environment.