The yellow vein mosaic disease infected mesta samples exhibited positive amplification with different primers specific for coat protein (CP) gene of DNA-A molecule of begomoviruses and full-length DNA beta molecule. The amplified product of a full-length DNA beta and the CP gene of two different isolates were cloned and sequenced. The DNA beta molecule was 1,354 nt in length having highest sequence identity (86.1%) with two reported DNA beta molecules of Indian isolates of begomovirus infecting cotton (accession number DQ191161 and AJ316038). Highest sequence identity (85.5%) of betaC1 gene product was found with that encoded by DNA beta associated with begomovirus infecting tomato (AJ316035), originating from Pakistan. The predicted betaC1 protein consisted of 118 amino acids. The nucleotide sequences of the CP genes from both was 771 nt in length and showed sequence identity with CP genes of begomoviruses infecting tomato (82.2-92.4%), tobacco (AY007616, 94.2%) and Croton (AJ507777, 93.9%). The highest percentage sequence identity (97.6%) of the CP gene product was found with that encoded by DNA-A of two isolates of begomovirus infecting tomato (AJ810364 and AJ810357). The predicted CP consisted of 256 amino acids. The results indicate for the first time that the begomovirus associated with mesta yellow vein mosaic disease contains DNA beta molecule along with DNA-A in its genome. The phylogenetic tree also indicated that the DNA beta molecule reported here is distinct from other known geminiviruses or nanovirus components.