Tomato yellow leaf curl virus (TYLCV) and other members of the genus begomovirus are major constraint to tomato production in Oman. They are either bipartite (DNA-A and DNA-B) or monopartite (DNA-A). Monopartite begomoviruses have six Open Reading Frames (ORFs), among them coat protein gene (ORF-V1) and Rep gene (ORF-C1) are encoded on virion sense strand and complementary strand, respectively. Tomato yellow leaf curl disease is caused by a complex of TYLCV species as well as other begomoviruses. The objectives of this work are to determine the diversity of begomoviruses and associated betasatellite in tomato crop, to study the role of betasatellite associated with tomato begomoviruses in symptom development and to elucidate the role of TYLCV-OM ORF-V1 and ORF-C1 in pathogenesis. Symptomatic tomato leaves were collected from different Welayat and total genomic DNA was extracted. The viral DNAs were amplified using Rolling Circle Amplification (RCA). The viral genomic components were cloned using unique restriction endonucleases and were completely sequenced. Agroinfectious constructs of TYLVC-OM DNA-A and DNA-B were made in a binary vector. Their infectivity was checked individually as well as in different combinations on tobacco and tomato plants. Site directed mutagenesis on ORF-C1 and deletion mutagenesis on ORF-V1 were performed. The infectivity of the mutants was tested by Agro-inoculation and symptom development was compared. Five different begomoviruses were found to be associated with tomato in Oman. Tomato yellow leaf curl virus strain Oman (TYLCV-OM) was found to be confined to the northern governorates of Oman. Tomato leaf curl Al Batinah virus (TOLCABV), the recombinant between Chili leaf curl virus strain Oman (ChLCV-OM) and Tomato leaf curl Oman virus (TOLCOMV) was found to be confined to Al Batinah governorate in the Northern part of Oman. TOLCOMV was also found to be confined to Al Batinah. TOLCSDV was found in Dhofar, the Southern governorate and Manah of A'Dakhliah governorate in the North. However, Chili leaf curl virus strain Oman (ChLCV-OM) was found to be associated with tomato in all governorates of Oman. TYLCV-OM, TOLCOMV and ChLCV-OM were found to be associated with betasatellite. On the other hand, TOLCABV and TOLCSDV were not found to be associated with betasatellite. Betasatellite was found to be able to interact with these begomoviruses and change the phenotype of the symptoms. ORF-V1 and ORF-C1 of TYLCV-OM were found to be essential for pathogenicity of the virus. The data presented here is the first comprehensive study of begomoviruses and their associated betasatellite and suggest that begomoviruses of diverse origins were introduced into Oman through trade and these viruses are rapidly evolving by recombination.