A synchronizing method and a system for marks on electronic maps and a recording medium using the same are provided. In the present synchronizing method, an input signal is received by a first electronic device, so as to draw a mark on the electronic map displayed thereon. The mark is then converted into positioning information of a plurality of positioning points on the electronic map and transmitted to a second electronic device via a wireless transmission network, wherein the positioning information is used for drawing the positioning points on the electronic map displayed on the second electronic device so as to reconstruct the mark. Accordingly, the mark on the electronic map of both communication ends can be synchronized.