Major explosive outbreaks of Rift Valley fever (RVF), an arthropod borne zoonotic disease, occur in humans and animals with significant mortality and economic impact across continental Africa and the Indian Ocean region (Madagascar, the Comoros archipelago). Recently, sporadic human cases have been reported in Mayotte and Grande Comore, two islands belonging to the Comoros archipelago. To identify the hypothetical source of virus introduction in an inter-epidemic or a post-epidemic period, a longitudinal survey of livestock was set up in Comorian ruminant populations, known to be susceptible hosts. The phylogeographic genomic analysis has shown that RVF virus (RVFV) detected in a zebu collected in Anjouan in August 2011 seems to be related to the last known epidemic of RVF which occurred in East Africa and Madagascar (2007–2009). This result highlights the fact that RVFV is maintained within local livestock populations and transboundary animal movements from eastern continental Africa to Indian Ocean islands likely result in RVFV crossover.