The Emission Trading Scheme for green house gases is a key too of European climate protection. Including the road transport sector might be a promising strategy to limit its CO2 emissions. This could be realized within a common market (trans-sectoral trading permitted) or separated markets (trans-sectoral trading not permitted). Starting from different assumptions on emission deduction objectives, the impact of both options is analysed using a quantitative model. Although an emission trading scheme is ecologically effective regardless of the trading model, it turns out that CO2 emissions and emission allowance prices differ strongly between both design options due to sector specific price elasticities of allowance demand.