The Madura Strait area is one of the busiest marine traffic regions in Indonesia. Many ships arrive, depart and travel through that area, thus influencing the air quality of the port environment. Furthermore, the Indonesian government has not yet ratified Marine Pollution (MARPOL) 73/78 Annex VI regarding the prevention of air pollution from ships and the absence of restricting regulations could have an influence on the level of air pollution. In this study, an Automatic Identification System (AIS) receiver is used to obtain ship data. AIS recognizes a vessel's Maritime Mobil Maritime Identify (MMSI), speed of ship, initial position of ship and ship type. This data is used to evaluate the marine traffic density in the Madura Strait area. Information from ship databases and AIS data are combined for retrieving gross tonnage (GT) information, which is then used to estimate the ship's air pollution emissions. Air pollution estimates also consider the ship's operation modes such as berthing, maneuvering and hotelling. The basic aims of this study are to evaluate marine traffic contributions to the nitrogen oxides (NOx), sulfur oxides (SOx), particulate matter (PM), carbon monoxide (CO) and carbon dioxide (CO2) levels in the Madura Strait area, and to evaluate the possibility of using AIS data when estimating air pollution levels. The emission quantities of NOx, SOx, PM, CO (as indicators of air pollution) and CO2 (as a greenhouse gas) are shown in this paper. The process for estimating emissions using AIS is a potential decision-making tool when considering issues such as the effects of ship emissions on health is also evaluated.