A method and system for synchronizing two computer systems supporting multiple synchronization techniques is described. In one example system, a portable computer system is loaded with synchronization transport modules. An application on the portable computer system is executed causing the application to automatically recognize the synchronization transport modules. The portable computer system receives a selection corresponding to one of the two synchronization transport modules. The selection could be from a user and would indicate that the user prefers to synchronize with the second computer system using a particular method of external communication. After the selection, the portable computer system synchronizes with the other computer system using the selected method of external communication.