Pollutants from fishing boats have generally been neglected worldwide, and there is an acute shortage of measured emission data, especially in China. Therefore, on-board measurements of pollutants emitted from 12 different fishing boats in China (including gill net, angling, and trawler boats) were carried out in this study to investigate emission factors (EFs), characteristics and total emissions. The average EFs for CO, CO, NO , PM, and SO were 3074 ± 55.9, 50.6 ± 31.7, 54.2 ± 30.7, 9.54 ± 2.24, and 5.94 ± 6.38 g (kg fuel), respectively, which were higher than those from previous studies of fishing boats. When compared to medium-speed and slow-speed engine vessels, high-speed engines on fishing boats had higher CO EFs but lower NO EFs. Notably, when fishing boats were in low-load conditions, they always had higher EFs of CO, PM, and NO compared to other operating modes. The estimated results showed that emissions from motor-powered fishing boats in China in 2012 (232, 379, and 61.8 kt CO, NO and PM) accounted for 10.7%, 10.9%, and 19.3% of the total CO, NO and PM emitted from nonroad mobile sources, which means significant contribution of fishing boats to air pollution, especially in southern China areas.