The article describes the rationale for the development of an information system in order to perform the tasks of Rosselkhoznadzor on the analysis of phytosanitary status of territories, which includes planning and results of plans for quarantine phytosanitary monitoring of territories, results of phytomonitoring of pests of quarantine importance for major importing countries of Russian grain and analysis of quarantine phytosanitary status of territories. Functions, structure and information objects of this information system, roles of information system users are described. The results of information system implementation in the practice of the Russian Plant Quarantine Service are evaluated, such as increase of efficiency of the Rosselkhoznadzor function on control and supervision in the field of plant quarantine, ensuring compliance with quarantine phytosanitary requirements of importing countries, which significantly increased the export potential of the Russian Federation, significantly reduce the risk of damage caused by the spread of quarantine objects on the territory of the Russian Federation.