Environmental Impact Assessment Law executed in Japan in 1997 has a special- feature: evaluation of biodiversity in ecosystem, level. However, a standardized methodology has not yet come to an agreement. It would be informative for building a reliable evaluation method that properly value biodiversity in ecosystem level to review the recent research products and make its problems clear. Putting a special focus on 25 major journals published after 1995 including Ecological Applications, Biological Conservation, Landscape and Urban Planning, and Ecology, I have searched and analyzed evaluation models for biodiversity in ecosystem level. Based on factors that evaluation models put attention to, they were classified into three major categories; i.e., compositional, structural, and functional models. Taking a final evaluation value into account., father three subdivisions were detected; i.e., absolute value, index and ranking. In results, four challenges to establish evaluation methods accounting for biodiversity in ecosystem level were clarified, i.e.; (1) Different guilds, species or populations in the same level of food pyramid and depend on the same resources, and species groups that maximize the phylogenetic diversity should be selected as surrogate of ecosystems.(2) Extinction risk of the selected organisms should be assessed by Population Viability Analysis.(3) It is necessary to identify potential habitat area by Potential Habitat Analysis; quantitative analysis of species distibution pattern and environmental pattern that is strongly correlated to it.(4) Survival probability in the potential habitat area should be quantitatively estimated by relating parameters of population dynamics with environmental attributes of potential habitat area.

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