According the IMO(International Maritime Organization), more than 10 billion tons ballast water was transported, with more than 7 000 species with the ship ballast water migration in the global scope. In order to assess the risk of being "invaded" by alien organisms in Shanghai and the surrounding sea areas and to investigate pathogenic microorganisms in ballast water from International ships sailing to Shanghai, we have collected ballast water samples from ships berthed in Yangshan port,Chongming port and Waigaoqiao Port for detection. Sample preparation,incubation and detection and identification are operated as the government standard GB/T5750. 12-2006 and Standards for Drinking Water Quality(2001). The results showed some Aeromonas and Enteropathogenic Monoucleosis were detected, including Enterococcus casseliflavus. The total bacterial count of all the ballast water samples was in the range of 10³-10⁴ cfu/ml. Coliform was found in 4 samples from 3 ships,while Vibrio cholera had not been detected. The result demonstrated the risks of pathogenic microorganism in the ballast water of the ships at the Shanghai Port, which warns us to strengthen the management of ballast water. For newly detected pathogenic bacteria, detecting methods and standards should also be established.For the strategy to International Convention for the Control and Management of Ships' Ballast Water and Sediments, we should do more survey and collect more data for more detailed assessment about the risk of the incoming ships's ballast water.