In complex food webs, species often interact with each other indirectly through mediating species. As a result of geographic mosaic of coevolution, such interactions are often evolutionarily unstable and the traits governing the interaction sometimes vary over time. A common example is the interactions between hosts and endoparasitoids, in which the phenotypic variation has been studied in terms of both host immunity and parasitoid virulence. This thesis focuses on characterizing the genetic background underlying the coevolution between host immune response and parasitoid virulence in a host-parasitoid interaction system. For this purpose, I used Galerucella-Asecodes system, which contains three leaf beetle species (Galerucella calmariensis, G. pusilla and G. tenella) and their shared parasitic wasp, Asecodes parviclava as the study model. By integrating next generation sequencing techniques and ab initio evidence-driven annotation approach, I generated genome assemblies and annotation of both the wasp and the three Galerucella species (Paper I & IV). In order to study variation in immune capacity at the expression level, I de novo assembled and annotated the transcriptome of G. pusilla and G. calmariensis, which have contrasting immunocompetence against the Asecodes wasp (Paper II). Using a time-course differential expression analysis, I investigated gene expression in parasitized larvae of G. pusilla and G. calmariensis after the wasp attack, and suggested that signaling and hematopoiesis genes play a key role in the host immunity in Galerucella against wasps (Paper II). Using comparative analysis of Galerucella species, I identified important genes and pathways under natural selection which potentially explain the divergence in their morphology and immunity (Paper III). I also focused on the geographic variation in the Asecodes wasp using population comparisons and identified several candidate regions of the genome for host adaptation. We also detected that genes involved in the inhibition of host immune systems and odorant/gustatory receptors are associated with variation in virulence (Paper IV).