Clematis (Clematis spp., family Ranunculaceae) is a perennial climbing plant widely used in landscape design. Over 120 local and introduced clematis cultivars are maintained in the field collection of the Nikita Botanical Gardens, Yalta, Russia. Plants displayed leaf chlorosis, mottling, mosaic, and vein yellowing. Next generation sequence analysis of 8 individual or bulked samples representing 20 cultivars, one plant of each selected cultivar, was performed regardless of symptoms. From a single plant of cultivar Valge Daam, 2 500 reads from a total of ∼59 million reads mapped to plant virus sequences related to Moroccan pepper virus (MPV, genus Tombusvirus). Reverse transcription-PCR using total RNA extracted from the presumably infected plant and four MPV-specific primer pairs confirmed the presence of the virus. Using the NGS data, the full-size genome of the Russian MPV isolate (named MPV-Cl) was assembled and the sequence has been deposited in GenBank (MG250195). Phylogenetic analysis of the tombusvirus complete genomes assigned MPV-Cl to a separate cluster consisting of the MPV isolates with 100% bootstrap support. To date, MPV has been reported to infect pepper, tomato, pelargonium, eggplant, escarole, lisianthus, pear, and lettuce, and can persist in soil water and plant debris. This is thought to be the first report of MPV infecting clematis in Russia and worldwide.