Tomato yellow leaf curl disease (TYLCD) is caused by two begomovirus species (Geminiviridae, ss circular DNA), Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) in the Mediterranean region. Interspecies recombinants were frequently reported in both naturally infected tomato plants and in plants co-inoculated with TYLCV and TYLCSV. The TYLCV/TYLCSV recombination profiles were relatively homogenous with a recombination breakpoint (RB) always located at the origin of replication (OR), and other RBs distant from the OR. None of these recombinants has been reported to be associated with breaking of the resistance induced by the Ty-1 resistance gene which is virtually present in all TYLCD-resistant tomato cultivars used in the Mediterranean. Unusual recombinants for which the non-OR RB was very close to the OR were detected in Ty-1 tomato plants in Morocco (TYLCV-IS76) and Italy (TYLCV-IS141) and exhibited invasive and Ty-1 resistance breaking features. Unlike TYLCV-IS141, TYLCV-IS76 was not positively selected in tomato plants co-inoculated with TYLCV and TYLCSV, which suggest that their generation and pre-emergence in natural conditions was probably different. However, both recombinants were shown to have a selective advantage in Ty-1 plants with a tremendous negative impact on the accumulation of TYLCV, the most competitive parental virus. This advantage was shown to be associated to the short 76-nt TYLCSV inherited fragment. The molecular determinism of the competitiveness of these recombinants was investigated according to three hypotheses: (i) the replication of the recombinants may be more efficient due to their 8 nts shorter genome in the recombinant region, (ii) a lower GC content which may reduce the transcriptional gene silencing which is expected to be involved due to the RNA dependent RNA polymerase encoded by Ty-1, and (iii) the TYLCV region that was switched in the recombinants has relieved the genome from a fitness l