Agriculture, forestry, fisheries and food industries have underpinned the Japanese diet. They have also provided Japanese society with the basis for its living environment and cultural activities. However, growing concern over global environmental problems urges the adoption of effective measures for the reduction of environmental burdens in primary industries. Domestic trade among metropolitan and local regions has strongly affected the environmental loads created by agriculture, forestry, fisheries and food industries. Consequently, analyses of regional interdependence in transactions involving agriculture, forestry, fisheries and food industries are necessary to clarify the regional structure of environmental burdens attributable to these industries. Ecological footprint (EF) analysis, as developed by Mathis Wackernagel and William E. Rees at the University of British Columbia, is a useful tool to identify human demands on the Earth's ecosystems and environmental interdependence among regions. Despite its theoretical criticisms, EF analyses are widely used to evaluate environmental burdens created by human demands on nature. This paper proposes an analytical method combining the EF analytical framework with the regional input-output analysis to assess environmental interdependence among regions. The empirical studies use input-output tables and agricultural statistics of Japanese regions for 1990, 1995 and 2000. Finally, we conclude with a discussion of problems with EF analysis based on results of CO2 emission analyses. JEL classification: C67, O13