The non-indigenous species (NIS) via ship's ballast water in recent years has become an emerging problem around the world. We analyzed the shipping data of visited vessels in Port of Taichung from 1996 to 2008, and estimate the maximum ballast water discharge in the harbor. It was found that most of the ships visited Port of Taichung are registered under the flag of Panama and the last call of port were among the harmful algae bloom frequently reported country mainly from Asia region, especially Japan. The estimated ballast water discharge in Port of Taichung is around two million tons. We also proposed a sampling procedure by referencing the IMO (International Maritime Organization) guideline.