Air pollution is one of the most important branches of environmental science as it affects human health, climate and ecosystems. Emissions of air pollutants from transport (vehicles and ships) in port cities strongly affect air quality at local scales, warranting for a combination of theoretical and experimental studies to identify pollution hotspots. The purpose of this paper is to provide a methodology for developing a hybrid emission inventory from transport sector for two port cities located respectively on the Northern Aegean islands of Chios and Lesvos. Emission inventories were constructed for the year 2014 based on top-down and bottom-up approaches. Official data from local authorities and survey results were used for the calculation of emissions. Traffic emissions were spatially allocated to the road network based on population data and hourly traffic counts, and distributed over time (on an hourly basis) with the use of local temporal coefficients. Regarding carbon monoxide road emissions, the highest quantities are mainly emitted by Passenger Cars (43%,32% in Chios and Lesvos respectively) while for PM10 emissions, trucks have the largest share (66% in Chios and 86% in Lesvos). The pollutants that are emitted in greater quantities from the ships at the ports of Mytilene and Chios are NOx, followed by SO2 and CO. Most of the ship emissions in the ports occur by the ships at berth, as they remain berthed for hours whereas maneuvering lasts 15e20 min. As for the daily contribution of the two transport sources to the pollution profile of Mytilene, road emissions are higher for almost all pollutants. However, the contribution of ship emissions is not negligible, especially during the touristic period when marine traffic increases and emissions close to the port area become more important than those from road transport.