According to the mid-term review of the EU White Paper on Transport, Short Sea Shipping is expected to grow at a rate of 59% (metric tonnes) between 2000 and 2020. Even with Marpol Annex VI [1] in operation, the share of emissions from maritime transport can no longer be ignored because they would become increasingly important. There is an existing need to evaluate the impact of the maritime transport on air quality. This paper analyses emissions of maritime transport in SW European Short Sea Shipping, considering actual routes and ships’ particulars and presents the comparison of two emission models to calculate emissions from vessels, the REALISE [2] and the MOPSEA [3] emission models. This paper will compare both methods and will conclude proposing some results that would justify the need to reduce atmospheric emissions from sea-going vessels to compete with road transport mode. Policy makers have to be aware of the results of such comparison and its effect on the current legislation for maritime transport.