Abstract: Background: Whitefly Transmitted Begomoviruses (WTB) cause worldwide economic losses. The WTB have either a monopartite or bipartite genome. The WTB in Egypt have monopartite genome. Recently betasatellite DNAs were found associated with WTB in Egypt. The bipartite squash leaf curl virus was recently introduced into Egypt (SLCEGV). Materials and Methods: The incidence of WTB, associated betasatellites and the incidence of SLCEGV was examined in different crops in Egypt for over 4 years. Rolling Circle Amplification (RCA), Polymerase Chain Reaction (PCR) and RCA-random fragment length polymorphism (RCA-RFLP), DNA sequencing and phylogeny analysis were used to study the nature of WTB and associated betasatellites in Egypt. Results: Disease symptoms ranged from leaf curling, rugosity, vein yellowing, vein enlargements, mosaic, leaf enations and yellowing. The number of identified WTB was limited to few monopartite WTB and one bipartite WTB. The PCR of RCA products indicated the presence of DNA-B components in several tested samples other than SLCEGV. The RCA-RFLP revealed the presence of several digested products ≥5 kbp in several tested samples with presence of SLCEGV in non-host or presence of other unknown bipartite begomoviruses. Betasatellites were associated with both mono and bipartite WTB and proved to be host-promiscuous in distribution. Phylogenetic analysis involving SLCEGV and the monopartite begomoviruses showed possible genomic mixing. Conclusion: The SLCEGV has increased the biodiversity in area with limited biodiversity. Evidence suggests genomic mixing between the local WTB and SLCEGV and possible acquisition of new betasatellites by SLCEGV that may modify viral virulence and fitness.