Begomoviruses (Geminiviridae familly) cause many disease outbreaks all around the world in a large variety of crops. Previous studies have shown the high diversity of these viruses and the importance of recombination in their evolution (Paddidam et al., 1999). To better understand the evolutionnary mechanisms of Begomoviruses, a study of the diversity of indigenous monopartite begomovirus in the South West Indian Ocean (SWIO) islands was done.