Chili leaf curl virus (ChLCV) and Tomato leaf curl virus (TYLCV) are members of Genus Begomovirus (family Geminiviridae) which contains single–stranded DNA viruses transmitted exclusively by the whitefly (Bemisia tabaci). An analysis of the genetic diversity of begomovirus isolates across Oman was conducted. A total of twenty five samples were collected from different governorates (Muscat, Musandam, Ad-Dakhilia, Al-Batinah South, Dhofar and Ash-Sharqiah South) and were tested for begomovirus, betasatellite and alphasatellite molecules. Rolling circle amplification (RCA) was used for the detection of full-length begomoviruses, while polymerase chain reaction (PCR) was used for the detection of betasatellite and alphasatellite. The complete nucleotide sequence identity of the begomoviruses, alphasatellite and betasatellite were done in their entirety. Analysis of these sequences showed that ChLCV and TYLCV are the most prevalent causal agents of leaf curl disease in Oman and show phylogeographic segregation. Moreover, ChLCV was characterized from a new weed host Senna italica Miller located near an infected tomato field. Further it was found that the amplified ChLCV and TYLCV exhibited the highest nucleotide identity with the previously reported ChLCV and TYLCV strains infecting tomato in Oman. Although, earlier studies have indicated that TYLCV is the most prevalent virus infecting mainly tomato crop in Oman, this study shows that ChLCV has been increasing its host range into diverse host plants including weeds as well as increasing its distribution into diverse geographical areas. Furthermore, phylogenetic and other molecular analyses showed that 88% of tested plant samples with begomovirus-like symptoms were also associated with tomato leaf curl betasatellite. In addition, the occurrence of alphasatellite is very rare, and only one okra leaf Oman alphsatellite was also detected.