Captain is a key player for controlling the commercial shipping and has the major role in dealing with the occurrence and process of stowaway case. His decision on handling the stowaway is often complicated by the unnecessary legal issues if it is not following the normal process such as the violation of unlawful action on processing the stowaway issue. The stowaway case always has been a serious problem in commercial shipping. It often causes unnecessary legal issues for shipping owner and captain because of unwise decision from the ship captain. Since the occurrence of 911 terrorism in 2001, International Ship and Port facility Security Code (ISPS Code) has adopted more restrict security code on the prevention of stowaway, but it has indirectly resulted in the tendency toward underground and better organized shipping stowaway crime. This change has also provided guidance for captain¡¦s decision on the process of stowaway case. The present study illustrates two important stowaway cases occurred at Taiwan commercial shipping lines. One is related to liner, the Maersk Dubai, and the other is for tramp, the Well Pescadoies. The present study made comparison on both case handling processes and their treatments on stowaways and the problems of derived legal actions resulting from the unwise and unnecessary actions from the ship captains. The study adopted the person to person interview results and discussion with ship captains, literature search, and case legal documents for analyzing the possible process problem of stowaway associated with both cases. The present study summarized the precautionary approaches and guidance for ship owner and captain on the prevention of stowaway and the requirement of ISPSC code including related IMO convention, protocol, and regulation. Other main concerns are how to promote the shipping security including the duty of captain and the interests of shipping owner.