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This article examines the possibility to assimilate vessel positional data of the Automatic Identification System (AIS) into the Fishery Monitoring System (FMS). One of the main features of FMS is remote control of Russian and foreign fishing vessels locations. Positional data enter FMS via the channels of satellite systems Inmarsat and Argos. However, these satellite systems have a number of disadvantages. Many of them can be overcome by integration with AIS operating in VHF band. AIS features stable and reliable performance at high data transfer rates and minimal traffic costs of vessel location reporting. In this article, a method of positional data integration by comparing vessel IDs in both systems is discussed. The proposed algorithm of “search for a match” for vessel IDs in AIS and FMS systems by vessel tracks provides significant reduction of computation costs for this integration method and high reliability of vessel IDs matching in both systems. Moreover, it is shown that the proposed algorithm can also provide additional information unobtainable by merely matching the AIS and IMS vessel symbolic data.