Begomovirus are wide genera of plant viruses with circular, single-stranded DNA genomes packaged within geminate particles and transmitted by the whitefly Bemisia tabaci. In the South West Indian Ocean (SWIO) islands, the importance of begomovirus diseases is increasing and has spread on many host species since the introduction of a very polyphagous biotype of the insect vector. Within the Regional Program of Plant Protection, an inventory of plant pathogens was organized in the islands of the region, in particular on the Comoros islands where we found tobacco plantations showing severe symptoms of leaf curling. After complete DNA virus genome cloning and sequencing, we identify three begomovirus species: the Tomato leaf curl Mayotte virus, the Tobacco leaf curl Zimbabwe virus and the third that is a new species, temporary named the Tobacco leaf curl Comoros virus. Complete DNA genome sequences were analysed with RDP2 package (Martin et al., 2005) and suggest that the TbLCKMV is a recombinant virus between ToLCYTV and TbLCZV. Sequences were also analysed with PhyML and MrBayes for phylogenetic studies. In order to test the symptomatology (severity) and the differential host range, we produced infectious clones.