Nowadays maritime data communications are mainly performed by satellite and radio media. But these media have limits on economics or data rate. Future ships at sea would need broad and stable maritime data communication system like that of land. Today, AIS (Automatic Identification System) and Mavlink (Micro Air Vehicle Link) is one of the exist system that can be used to support those activities. AIS is a system that tracks the ships position automatically, control the ships condition and collision avoidance in all ports. Mavlink is a protocol for communication with unmanned vehicle as in charge to build the link connection, Provide logic procedure for information transfer, and link connection. This research carried out the protocol performance comparison between AIS and mavlink to contrast performance of receiver on ship under 30 GT (Gross Tonnage). The researcher did not conduct directly research in the field due to the trial result of distance has maximum at 103 while in the field needs greater distance mavlink Protocol will work on transmission condition of half duplex. The physical layer and data link layer on protocol can be divided into several status condition. It means the condition is to define the condition of radio communication link for multi link. The test result of transmission distance variation demonstrated that the further distance transmission caused greater potential packet loss, the distance test at 90.8 m obtained packet loss at 11 packets while at 30.5 m transmission distance gained 1 packet loss. It can be concluded that the use of mavlink protocol can be used in custom compared to AIS protocol. Mavlink protocol in establishing the payload, can be arranged as its needed. While the AIS protocol is necessary to follow the predetermined standard. The establishment of payload protocol mavlink data can be arranged in payload at location bytes 1 until 32, the data bytes size highly determine the location determination on the payload.