The innate immune system ofDrosophilais activated by ingestion of microorganisms.D. melanogasterbreeds on fruits fermented bySaccharomyces cerevisiae, whereasD. virilisbreeds on slime flux and decaying bark of tree housing a variety of bacteria, yeasts, and molds. In this study, it is shown thatD. virilishas a higher resistance to oral infection of a species of filamentous fungi belonging to the genusPenicilliumcompared toD. melanogaster. In response to the fungal infection, a transcriptome profile of immune-related genes was considerably different betweenD. melanogasterandD. virilis: the genes encoding antifungal peptides, Drosomycin and Metchnikowin, were highly expressed inD. melanogasterwhereas, the genes encoding Diptericin and Defensin were highly expressed inD. virilis. On the other hand, the immune-induced molecule (IM) genes showed contrary expression patterns between the two species: they were induced by the fungal infection inD. melanogasterbut tended to be suppressed inD. virilis. Our transcriptome analysis also showed newly predicted immune-related genes inD. virilis. These results suggest that the innate immune system has been extensively differentiated during the evolution of theseDrosophilaspecies.