Grain legumes are an important source of dietary protein across southern Asia, but they suffer extensive losses due to several viruses that are members of the genus Begomovirus (family Geminiviridae), which are collectively known as legume yellow mosaic viruses (LYMVs). Despite their economic importance, little attention has been paid to LYMVs in Pakistan and only partial sequences of virus isolates originating from this country are available in the databases. Here, a survey of LYMVs occurring across Pakistan is described. Complete sequences of 44 components (23 DNA-A, 19 DNA-B and 2 betasatellites) were determined. The results show that only the mungbean yellow mosaic India virus (MYMIV) is of agricultural significance in Pakistan having been isolated from all cultivated grain legumes examined. Mungbean yellow mosaic virus, a significant crop pathogen in India, was only identified in a weed, which together with a novel species of LYMV we reported earlier, represents the first LYMV identified in non-cultivated plants. MYMIV was shown to occur as two types in Pakistan that show phylogeographical segregation. Additionally, two begomovirus species not considered pathogens of legumes and a betasatellite were isolated. This is of grave concern since it suggests that the presumed genetic isolation of the LYMVs in legumes may be being breached. LYMVs show little, if any, evidence of interspecific recombination with non-legume infecting begomoviruses. Thus, either recombination with non-legume viruses or interaction with betasatellites, which are host range and pathogenicity determining satellites of begomoviruses, could lead to the appearance of more aggressive virus variants/strains affecting legumes.