The complete genome sequence of tomato leaf curl Palampur virus (ToLCPlV), that infects a papaya (Carica papaya) plant, was determined. The virus genome was composed of 2,756 and 2,719 nucleotides (nt) in length, encoding all proteins required for replication, encapsidation and movement with the genome features typical of a bipartite begomovirus. Pairwise identity, derived using the Sequence Demarcation Tool (SDT), identified that the virus DNA A and DNA B shared maximum sequence identity 98–99% corresponding to the DNA A of ToLCPlV ([IR: Jir-T65X:08] JF501720) and 96–98% to the cognate partner DNA B of ToLCPlV ([IR: Jir1:T55P:07] FJ660423), respectively. The evolutionary relation using phylogenetic dendrograms of DNA A and DNA B genome components were clustered with ToLCPlV genomes of DNA A and DNA B of Iranian isolates. This study provides the first evidence of a bipartite ToLCPlV infecting papaya in the Sultanate of Oman and also indicates the requirement for more surveillance of this virus in Oman, as ToLCPlV is a major threat to tomato and other vegetable crops in South Asia (India and Pakistan) and in Iran.