Tomato leaf curl New Delhi virus (ToLCNDV), a bipartite begomovirus (family Geminiviridae), has emerged as a significant threat to global agriculture due to its broad host range, rapid geographical expansion, and high genetic variability. This study integrates phylogenetic, pairwise divergence, and selection pressure analyses to elucidate the evolutionary dynamics of ToLCNDV. Full-length DNA-A and DNA-B sequences, along with the CRESS domain of the replicase gene, were evaluated using the sequences obtained from NCBI across 24 countries. Phylogenetic clustering revealed 19 DNA-A and 24 CRESS-based clades, with strong geographical and host-specific patterns such as Pakistan-dominated tomato isolates, cucurbit-adapted strains in Europe/Asia. Pairwise divergence highlighted extreme genetic diversity, with CRESS domain similarities ranging from 32.2% to 100%, compared to 56.4–100% for DNA-A. DNA-B exhibited higher nucleotide diversity (Pi = 0.114) than DNA-A (Pi = 0.063), reflecting divergent evolutionary constraints. Negative Tajima’s D and Fu and Li’s values across all genes indicated pervasive purifying selection and population expansion. These findings underscore that ToLCNDV evolutionary plasticity might be driven by host adaptation, recombination, and global trade-mediated spread, necessitating vigilant surveillance and tailored management strategies.