The genome sequence of a bipartite begomovirus was identified in an ornamental plant, Golden duranta (GD) (Duranta erecta) exhibiting crinkled leaves and apical leaf curling, collected from three districts Lucknow (Lko), Basti (Bas) and Deoria (Deo) of Eastern Uttar Pradesh, India. Three complete genome sequences of each DNA-A and DNA-B, were amplified by rolling circular amplification (RCA), cloned and sequenced. The analysis for both DNA-A and DNA-B revealed 91–99% nucleotide sequence identity to tomato leaf curl New Delhi virus (ToLCNDV). Phylogenetic studies revealed that all three ToLCNDV-A isolates form a separate clade, whereas, isolates of ToLCNDV-B clustered together with ToLCNDV-Chi- RKG2 (MT264782). Furthermore, when compared to other DNA-A and DNA-B, ToLCNDV-[GD-Deo-In] DNA-A showed the most recombination events. The nucleotide substitution rates of ToLCNDV-A and ToLCNDV-B were established to be 8.152 10− 4 substitutions site− 1 year− 1 and 6.684 10− 4 substitutions site− 1 year− 1 respectively. However, the transitional and transversal substitution rates were shown to be higher in DNA-B with a total number of mutations (η) 691 in comparison with DNA-A. The combined negative values of the neutrality tests, Tajima’s D and Fu and Li’s D*, indicate purified selection with low-frequency polymorphism. The dN/dS ratio for ToLCNDV-A and ToLCNDV-B revealed the selective control of evolutionary relationships. Our study supports the theory that begomoviruses have expanded their host range and that the fast evolutionary rates are mostly due to recurrent recombination and mutation. This is the first record of bipartite ToLCNDV infecting D. erecta in India.