Tomato yellow leaf curl virus (TYLCV) is a major tomato pathogen in Oman. It belongs to whitefly-transmitted genus, begomovirus in the family geminiviredae. However, little is known about its epidemiology, molecular characterization, strains, natural hosts and transmission to tomato varieties. Disease incidence was recorded as high as 100% in non protected tomato fields, whereas disease ranged between 1–20% in Agryi protected fields. Typical symptoms of upward curling and yellowing of the leaves were observed on tomato leaves and chlorosis of the intervein and the margin of the leaves of peppers. The symptoms on common beans were observed to be yellowing of the leaves. Total nucleic acid isolated from symptomatic and asymptomatic samples was used as a template to amplify core CP, satellite DNA (DNA-B) by polymerase chain reaction (PCR) using primers, FD-CP382/RD-CP-1038, and Sat01/Sato2, respectively and full length genome by rolling cycle amplification. The PCR amplifications yielded core CP gene ranging 620–720 bp from 53 symptomatic samples collected from different regions and ~1300 bp satellite DNA in 37 out of 53 samples tested. The complete DNA sequence (2765 nucleotides) of the monopartite genome of TYLCV isolated from Wylaiat of Liwa was determined. The circular genomic DNA containing six open reading frames (ORFs), of which two (V1 and V2) are located on the virion-sense strand and four (C1, C2, C3 and C4) on the complementary-sense strand. The ORFs are comparable to those of other whitefly-transmitted begomoviruses with a monopartite genome. Sequence comparisons of core CP gene (V1) of Omani isolates with each other and with that of other begomoviruses showed that all Omani isolates are related to each other and closer to the isolate of China. The sequence comparison of full genome with other begomoviruses showed more than 91% similarity with TYLCV from Iran (TYLCV-IR). The natural hosts of the TYLCV strains of Oman were determined by ELISA to be tomato, pepper, common bean, squash and cucumber. The vareital test shows that CLN2545B, CLN2948E, CLN2264G, CLN2264J and CLN2498D are tolerant to TYLCV. These varietes should be retested in another study to confirm the result and to be recommended for farmers.