The purpose of this study was to contribute to filling the knowledge gap in public opinion and knowledge about forest and its certification in Japan, as well as to identify key elements and the possible role of public opinion within integrated bottom-up policies, bridging the sectors of forest, environment and energy. This article compares the public opinion of two rural towns in Japan, one of which is located in northern Hokkaido, whereas the other town is located on the southern Main Island Shikoku. Both municipalities had been identified as an optimal case study location and selected because of their early decision to pursue forest management certification and because both towns had been awarded the status of a Japanese "Eco-Model Cities" - to encourage the creation of low-carbon communities - in 2008 and 2009. In order to test the basic knowledge and information needs of the public, a questionnaire-based drop-off survey was conducted in early 2007 and mid 2009 respectively among all households of the two rural towns. The questionnaire was divided into 5 sections (general info, forest, forest management, bioenergy, and information needs) in each of which up to 15 questions were asked with main focus on forest certification and biomass for bio-energy. The answers were made on a 4/5 point scale, or in dichotomous-choice form and analyzed by using SPSS. Gaining better knowledge about what the public thinks regarding bioenergy and the environment is seen to be crucial for the design of future policies for integrating a range of discrete and sectoral approaches such as energy supply-demand measures, energy-efficient buildings, traffic measures, waste disposal measures and forest protection. Finally, this study describes and interprets differences and similarities in the public opinion of both Eco-Model Cities in Japan where bioenergy production and forest management certification plays an important role. Forest certification and bioenergy from forest were identified as key elements for future integrated bottom-up policies that need to concentrate on facilitating the linkage between forestry and renewable energy as well as on promoting environmentally sound management and forest certification