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.