Various Wolbachia pipientis strains have been shown to confer antiviral protection after their host’s infection with RNA viruses. Such a phenotype is of particular importance as this endosymbiotic bacterium is estimated to infect a total of 40% of all arthropod species including insects that vectorize viral diseases of humans, animals and plants. So far the related mechanisms remain unknown and the level of protection and corresponding between-strain variations have never been described in a homogenous genetic host background. Further knowledge, however, is crucial to develop the idea of using Wolbachia as a biological pest control agent and to understand to what extent this phenotype contributed to the evolution of both Wolbachia and its hosts. We compared 19 different Wolbachia strains as to their ability to protect flies from Drosophila C Virus (DCV) and Flock House Virus (FHV) –induced mortality in the same Drosophila simulans genotype. In addition the viral titer was measured to determine whether the antiviral effect correlated with delayed virus accumulation. Finally the Wolbachia density was quantified, to check if there was a direct relation between the density and the level of protection the bacterial strain administered. Our results demonstrated that 9 out of 19 Wolbachia strains conferred antiviral protection and between-strain variations were explained by the Wolbachia density, with higher densities causing higher levels of protection. Furthermore, these differences in protection were correlated to within-host viral titers insofar as the viral load was significantly lower in flies harbouring protective Wolbachia strains, suggesting that protection is dependent on a mechanism of resistance common for both viruses.