TYLCV-IS76 is an unusual recombinant between Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) (Begomovirus, Geminiviridae). In contrast with the previously reported TYLCV/TYLCSV recombinants, TYLCV-IS76 has a typical recombination breakpoint (RB) in the intergenic region (at position 76), and has replaced its parental viruses in the Souss (Southern Morocco). The population shift coincided with the deployment of Ty-1 resistant tomato cultivars, and according to experimental studies, has been driven by a strong positive selection in tomato plants of the resistant cultivars bearing the Ty-1 gene. Although Ty-1 resistant cultivars are extensively used in the Mediterranean countries in which TYLCV and TYLCSV were reported, TYLCV-IS76 has not been reported outside Morocco. This, in combination with the non-canonical recombination pattern, suggests that its generation may not be straightforward, although TYLCV and TYLCSV are highly recombinogenic. Hence, the potential generation of the typical RB76 was investigated in Ty-1 resistant and nearly isogenic susceptible plants co-inoculated with TYLCV and TYLCSV clones. RBs were screened by direct sequencing of recombined DNA fragments amplified with TYLCV- and TYLCSV-specific primers located on both sides of locus 76. RB76 was detected from a few plants of both cultivars but remained at an extremely low concentration up to 365 dpi. This stands in striking contrast to the high fitness of TYLCV-IS76 in field and experimental conditions, but is consistent with its unique report from the Souss (Morocco) and its non-canonical recombination profile. It is thought that the emergence of TYLCV-IS76 has occurred by chance due to improbable conducive conditions. Interestingly, RB141, another RB of the intergenic region, was frequently detected among recombinant genomes, and most importantly was found to be positively selected in resistant plants. According to a preliminary survey, RB141 bearing rec