Abstract Equine infectious anaemia virus (EIAV) is the causative agent of equine infectious anaemia (EIA). It belongs to the Retroviridae family, genus Lentivirus. Clinical signs associated with the infection are mainly characterized by fever, anaemia, oedema and various signs of depression. Infected horses will never eliminate the virus and thus remain a reservoir for the virus even in absence of clinical symptoms. Viral transmission from one animal to another occurs mainly through blood, via insect bites and iatrogenic mode. Insects, mainly Stomoxys, serve as mechanical vectors (virus does not replicate in the insect) keeping the infectious virus in their mouthparts for few hours after biting. This mode of transmission promotes viral spread in horse population mainly during horse show. In 2007, 2008 and 2009, several EIA premises were reported in south east of France in two counties (Ardèche and Var). The aims of this study was to undertake the molecular characterization of viruses responsible of those EIA premises and compare them to strains described in the litterature. A total of 21 spleens coming from seropositive animals, tested by AGID test, were obtained (3 in 2007, 2 in 2008 and 16 in 2009). Total from DNA from 1 g of tissue was extracted. Those samples were tested by semi-nested PCR assay. Phylogenetic analysis were performed by amplification and sequencing of the Gag gene (1 400 bp). In 2007 and 2008 only one premise has been declared in the Ardèche county with 4 equids infected (2 donkeys and 2 ponies), those equids did not exhibit any clinical sign. The 2009 episode in the Var county was far more important. Indeed, more than 500 horses were placed under surveillance including virus detection and restriction of movement. Ultimately, 16 seropositive mainly asymptomatic horses, with only one animal declaring clinical EIA, were slaughtered. Three samples 2007, one from 2008 and 12 samples from 2009 gave a positive signal by amplification by semi nested-PCR. Phylogenetic reconstructions based on the 1400 bp gag sequences from 2007-2009 French cases and others from GenBank grouped the viruses in different clusters consisting of virus originated from North America, China and Europe. All EIA sequences characterized from 2007 to 2009 were not related to any of the group described previously. France is not free of EIA but the cases diagnosed are isolated and are mainly asymptomatic horses. This study showed for the first time that different isolates of EIA viruses are circulating in France. Moreover, those isolates have never been described previously in the literature.