Cucumber (Cucumis sativus; family Cucurbitaceae) plants exhibiting begomovirus-like symptoms such as yellowing, mosaics and stunting were studied using cloning, sequencing, Species Demarcation Tool followed by phylogenetic clustering. The complete genome of DNA-A showed maximum sequence identity of 98.7% with the corresponding DNA-A of an isolate from “Iran” strain of Watermelon chlorotic stunt virus (WmCSV). The DNA-B displayed 97.5% nt identity with the component of DNA-B of WmCSV from Iran, too. Our results confirmed that yellowing and mosaic symptoms of cucumber are associated with a bipartite begomovirus (WmCSV). This study is the first characterization of WmCSV in association with described symptoms in cucumber from Oman.