Parasites impose high selection pressure on host fitness and are thought to be a major selective factor that promotes the evolution of resistance in host populations. Much of the resistance is determined by genetic factors, however, it is unclear what genetic factors promote resistance to parasites. In this thesis, I used Drosophila melanogaster as a model system to study the genetic basis of resistance against RNA viruses. To understand the genetic basis of infection between different viral and Drosophila genotypes, I investigated two classic models, gene-for-gene and matching-allele models. These models consider that the outcome of the infection depends on the specific compatibility between host and parasite genotypes. Here, I demonstrate that the genetic background of flies explained substantially the resistance against the viral pathogen, which represents an exception to the genotype-by-genotype interaction models. Additionally, I developed an accessible and reproducible protocol to isolate and characterize RNA viruses from wild population of Drosophila. As a result of the protocol, two novel positive-stranded RNA viruses were isolated, La Jolla virus (Iflaviriade) and Newfield virus (Permutotetraviridae). Using RNA sequencing and a customised bioinformatics pipeline, I recovered partial viral genomes which were used to reconstructed their phylogeny. Then, I experimentally explored the impact of the newly isolated viruses on Drosophila infected with Wolbachia, a mutualistic endosymbiotic bacterium that protects the flies against RNA viruses. Furthermore, I determined the host range of these viruses infecting several Drosophila species of the Sophora group. In particular, I evaluated the potential of the novel viruses as biological control agents on the invasive species D. suzukii, one of the most important invasive pests of ripening fruits and wine production worldwide. Finally, I performed a genome-wide association analysis to investigate the genetic variation of resistance to the novel viruses using the Drosophila Genetic Reference Panel. The genome-wide analysis revealed a substantial genetic variation in resistance to the virus isolates, providing new insights into the natural genetic variation in resistance to viruses in Drosophila, and antiviral response in insects.