Taking into consideration the quality of air, it is necessary to ensure a continued reduction of the gaseous emissions that are produced by the maritime transport. The most effective solution of this serious worldwide problem is application of a suitable fuel mixture, which contains a bio-component, i.e. the biofuel. The presented scientific study is focused on influence of the biofuels on production of the gaseous emissions in the case of a diesel auxiliary engine, which is used in the ship transport. There were created various fuel mixtures with different content of the bio-component in order to investigate their emission characteristics. The individual experimental measurements were performed at the different engine loading levels and using a variable engine speed spectrum. The obtained results demonstrated a significant influence of the fuel mixtures on the whole combustion process, on the heat release process, on the pressure time behaviour as well as on the engine emission characteristics.