Maritime transport is the most environmentally friendly type of transport mode. However, ships' exhaust emissions affect negatively and considerably air quality and human health. Since ships release exhaust emissions to air on a large scale, IMO has adopted the Annex VI 'prevention of air pollution' from vessels' to the MARPOL73/78 Convention in 1997. This annex put limits on SOx NOx and PM emissions in both worldwide and Emission Control Areas (ECA) . Turkey also adopted MARPOL Annex VI, and expected that an ECA will be announced in Turkish territorial waters in near future. Additionally, regulations on ECAs force ship owners or managers to use alternative technologies or fuels in order to reduce ship emissions. In this study, ship emission reduction ways are analysed, especially low sulphur marine gas oil (MGO) and LNG as ship fuels for SECA. Environmentally, two subjects have been discussed which are: total emissions from ships passing through Turkish Straits, and how much emission reduction can be obtained if these ships would use LNG or MGO as fuel. Financially, external costs of ship emissions onto national economy and investment costs for ship owners for new LNG fuelled ships or retrofitting of existing ships have been analysed by using Payback Period and Net Present Value methods.