Two distinct viral genotypes were identified in the same tomato plant collected from Gezira, Sudan and are provisionally designated Tomato leaf curl Sudan virus (ToLCSDV-Gez) and Tomato yellow leaf curl virus-Sudan (TYLCV-SD). A third genotype was identified in tomato samples collected in Shambat, Sudan (ToLCSDV-Sha). The ToLCSDV-Gez and ToLCSDV-Sha isolates were approximately 90% identical, TYLCV-SD from Gezira shared approximately 93% identity with TYLCV-Mld. Recombination analyses identified two fragments in the ToLCSDV-Gez and TYLCV-SD genomes, providing evidence that these two genomes had undergone intermolecular recombination. A half unit size (737 nt) single-stranded satellite DNA was associated with ToLCSDV-Gez and TYLCV-SD.