Ship emissions have a significant contribution to the global emissions and have adverse effects to the environment and human health. This study investigates the effects of ultra-low sulfur diesel fuel on the gaseous and PM emissions of a ferry, experimentally. On-board emission measurements were carried out both for the main and auxiliary engines which are four-stroke medium speed diesel engines. The concentrations of NOx, SOx, CO, CO2, O-2, PM and HC were measured for various engine loads. The shaft power measurements were also performed. The weighted emission factors, monthly and annual emissions of the ferry are calculated using the experimental data. The weighted emission factors of NOx, SOx, CO, CO2, HC and PM emissions for the main engine are found to be 11.91 g/kWh, 0.10 g/kWh, 0.67 g/kWh, 611.14 g/kWh, 0.62 g/kWh and 0.079 g/kWh, respectively. For the auxiliary engine, the weighted emission factors of NOx, SOx, CO, CO2 and HC are respectively, 13.01 g/kWh, 0.11 g/kWh, 2.19 g/kWh, 641.69 g/kWh and 1.31 g/kWh. The amount of emissions from the ferry is found to be maximum in the summer season. The results show that the emission factors are the major parameter in the emission inventory studies and should be defined carefully. It is seen that the ship emissions, especially SO2 and PM emissions can be reduced substantially by using the ultra-low sulfur diesel fuel. Therefore, the sustainability of the maritime transport can be improved by utilizing the ultra-low sulfur diesel fuel for the propulsion of ships.