A total of 821 tissue samples from rodents trapped during field campaigns organized in Europe and Africa were screened for the presence of arenaviruses by molecular methods and cell culture inoculation when feasible. Two Mus musculus domesticus trapped in the southwestern part of France were infected with a potentially new strain of lymphocytic choriomeningitis virus (LCMV), here referred to as LCMV strain HP65-2009, which was isolated and genetically characterized by whole genome sequencing. Genetic and phylogenetic analyses comparing LCMV HP65-2009 with 26 other LCMV strains showed that it represents a novel highly-divergent strain within the group of Mus musculus-associated LCMV.