In contrast to the prevailing view that invertebrate immunity relies on broad-spectrum recognition and effector mechanisms, intrinsic genetic compatibility between invertebrate hosts and their pathogens is often highly specific in nature. Solving this puzzle requires a better understanding of the molecular basis underlying observed patterns of invertebrate host-pathogen genetic specificity, broadly referred to as genotype-by-genotype interactions. Here, we identify an invertebrate immune gene in which natural polymorphism is associated with isolate-specific resistance to an RNA virus. Dicer-2 (dcr2) encodes a key protein upstream of the RNA interference (RNAi) pathway, a major antiviral component of innate immunity in invertebrates. We surveyed allelic polymorphism at the dcr2 locus in a wild-type outbred population and in three derived isofemale families of the mosquito Aedes aegypti that were experimentally exposed to several, genetically distinct isolates of dengue virus. We found that dcr2 genotype was associated with resistance to dengue virus in a virus isolate-specific manner. By contrast, no such association was found for genotypes at two control loci flanking dcr2, making it likely that dcr2 contains the yet-unidentified causal polymorphism(s). This result supports the idea that host-pathogen compatibility in this system depends, in part, on a genotype-by-genotype interaction between dcr2 and the viral genome, and points to the RNAi pathway as a potentially important determinant of intrinsic insect-virus genetic specificity.