Only a few number of metagenomic studies concern plant viruses. However, a global knowledge of viral diversity would be very interesting in terms of ecology and could have important impacts on viral taxonomy and diversity studies and, potentially, on the prediction of emerging plant diseases. As an example, the “Plant Virus Biodiversity and Ecology” (PVDE) project has been initiated to survey the biodiversity of vascular plant viruses in the nature Conservancy’s Tallgrass Prairie Preserve of Oklahoma in USA (Wren et al., 2006). Our purpose is to describe the viral metagenome of the French sub-antarctic islands, especially in the Kerguelen islands. This project is included in the nationally funded EVINCE project “Vulnerability of native communities to invasive insects and climate change in sub-Antarctic islands” The ecosystems of these islands provide a suite of environments and scenarios that give key opportunities to improve our understanding of the consequences of climate change and biological invasions on terrestrial ecosystems. An additional interest is that almost nothing is known on the plant viruses present in such remote ecosystems, with the exception of a single report describing a new member of the Badnavirus genus (Skotnicki et al., 2003). Viral screening was done by two approaches. The first one, opened, consists in the analysis of double-stranded RNA, random cloning, sequencing, and comparison with sequences in databanks. By this approach we have been able to detect in an introduced Tropaeolum majus sample, sequences presenting 34% of identity in amino acids (56% of similarity) with the replicase of Oryza sativa endornavirus. The same approach permitted the identification of a new plant or fungal virus in a native plant of Kerguelen islands (Aceana magellanica). The sequences revealed 50% of identity with the capsid of Black raspberry virus F. The second approach consists in the screening of viruses belonging to known viral genera by polyvalent detection RT-PCR tests. One Tropaeolum majus sample was identified as being infected by a virus belonging to the Nepovirus genus. Indeed, the sequencing of the amplified fragment showed a significant identity in amino acids (89% and 93% of similarity) with the RNA-dependent RNA polymerase region of Cherry leaf roll virus (CLRV), a well known member of Nepovirus genus. Tropaeolum majus was known to be an experimental host of CLRV, but for our knowledge it is the first time that CLRV is described to infect naturally Tropaeolum majus. In this case, it seems that the virus was introduced in same time than the host plant, demonstrating, if necessary, the impact of species introduction on such terrestrial ecosystems.