Kaohsiung Harbor is adjacent of Kaohsiung City, a metropolis that has long suffered from air pollution. The annual releases of air pollutants such ad SOx, NOx, COx, PM, and HC from stationary and land-based mobile sources in Kaohsiung City have recently been thoroughly studied. However, emissions from vessels (another mobile source) have not been extensively investigated and understood. Evaluation ship emission in Kaohsiung’s harbor waters may be crucial to controlling air pollution in Kaohsiung city. This work, therefore, estimates the emission of air pollutants from in 1997 and evaluates their contributions to total emission in the city of Kaohsiung. Various approaches of estimation based on different databases and assumptions yielded different results. The emission of NOx, PM, HC, and CO were 13786, 341, 713, 1684, ton/yr, respectively, from vessels in Kaohsiung’s harbor waters, as estimated by Ship Operation method/Cargo method. Emissions of SOx and NOx were 4055 and 9125 ton/yr, respectively according to Lloyd’s emission factor/fuel consumption approach and emission of SOx and NOx were 4837 and 5114 ton/yr, respectively, according to ship exhaust measurement/calculation. The contribution of SOx and NOx from shipping in the Kaohsiung city area were significant. Around 10~20% of NOx and 10~12% of total SOx emissions in Kaohsiung city were attributed to ships in the harbor waters of Kaohsiung.