To secure resources, submarine environment should be firstly explored. On that occasion, the withdrawal of the instrument is important and the submarine ultrasonic wave should be stably identified regardless submarine environment and passive factor. In the existing control methods, the control informations, received from an observation instrument, are identified used by hardware and repeatedly compared with standard information. Hereupon, a marine observation instrument remote control system using the combination of FSK and ASK that was improved its controllability and movability was presented in this paper. Likewise, the logicality of communication algorithm were ascertained by experiments.