Non-indigenous aquatic species (NIAS) are those that can be introduced outside of their natural range or dispersal potential through intentional or unintentional introduction resulting from human activities. NIAS may be brought into another country during shipping by becoming attached to the ship hull or in the ballast water. Ballast water serves as a carrier for the introduction of NIAS and is associated with at least one third of the world's hundreds of marine biological invasions. In this study, the environmental similarity and the characteristics of vessel was used to establish a two-stage risk assessment for the incoming vessels to the port of Kaohsiung. The priority for PSC inspection can be established for better ballast water management.