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Not AvailableBegomoviruses infecting legumes (family 'Geminiviridae') pose a serious threat to the cultivation of grain legumes. Eventhough legume yellow mosaic viruses (LYMVs) cause significant loss in yield of legumes, studies regarding evolutionary lineage analysis of LYMVs are very rare. Previously, we have shown that Mungbean yellow mosaic virus (MYMV) and Mungbean yellow mosaic India virus (MYMIV) are major begomoviruses causing yellow mosaic disease (YMD) of soybean in India. In this study, complete genome sequence of begomovirus causing yellow mosaic disease of soybean in Central Indian region was characterized. Furthermore, whole genome sequences of legume begomoviruses [DNA A (108 isolates) and DNA B (89 isolates)] were analyzed to infer genetic diversity, gene flow and evolutionary lineage using nucleotide sequence-based computational approaches. Analysis of nucleotide diversity disclosed that LYMV population as a whole is diverse compared to MYMV and MYMIV. Test of neutral evolution also reiterates the operation of purifying selection and population expansion of MYMV and MYMIV. However, LYMVs as a whole, show decrease in population size and act of balancing or neutral selection. Genetic differentiation studies reveal greater diversity between MYMV and MYMIV. Frequent gene flow was detected between Dolichos yellow mosaic virus (DoYMV), Rhynchosia yellow mosaic India virus (RhYMIV) and other LYMVs. Recombinant events have been detected among LYMV species suggesting frequent genetic exchanges. Molecular phylogeny also revealed distinctness of Old World begomoviruses as New World begomoviruses formed a separate basal cluster. Hence, it is concluded that genetic exchanges are recorded among the LYMVs, and implications of breaching this seclusion is also discussedDSR 1.24/1