This study analyzes how advances in clean energy production technology have facilitated related economic development and intensified competition between clean energy sources and fossil fuels. A forecasting model, the Taiwan general equilibrium model-Clean Energy (TAIGEM-CE), is adopted to elucidate the role of wind, solar, tidal current, geothermal, algal biodiesel, biohydrogen, hydrogen fuel cell, biodiesel and bioethanol. Baseline results indicate that biohydrogen, hydrogen fuel cell, biofuels and wind perform satisfactorily when external support is unavailable. Additionally, strong governmental investment in clean energies significantly contributes to development of biodiesel, wind, biohydrogen and hydrogen fuel cell sectors. Results of this study provide feasible means of allocating resources to achieve a smooth transition to a clean energy economy, in which biohydrogen and fuel cell will play a prominent role. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.