Among more than 20 existing types of longspine sandbur, (Cenhrus longispinus (Hackel ex Kneuck.) Fernald), an annual cereal of North American origin, is of particular importance for the Russian Federation. This plant is widely distributed in temperate countries as a weed plant. It contaminates farm crops, vegetables and melons, vineyards and gardens. It is a quarantine object for the Russian Federation and the countries of the Eurasian Economic Union. On the territory of our country there are small disparate foci localized along railway lines and within urban areas. Identification of the object in the pre-generation state is difficult due to the morphological similarity of the weed with other grasses. For the early detection of the weeds, it is proposed to use a molecular genetic approach based on the use of ISSR markers. The purpose of this study is to search for molecular ISSR markers to differentiate species of the Cenchrus genus and identify the quarantine species of C. longispinus. The authors studied fifteen specimens belonging to eight species of the Cenchrus genus and obtained from the collection of the All-Russian Plant Quarantine Center (VNIIKR). To identify interspecific genetic diversity, a set of twentyone ISSR markers was used. Six of the markers showed polymorphism, which allows identifying the studied species of the Cen-chrus genus. The species-specific profiles of the amplicons of these ISSR markers allow identifying the considered species. For a number of markers, species-specific C. longispinus bands have been identified.