Quantitative genetics seeks to understand the role of allelic variation in trait differences. Introgression lines (ILs) contain a single genetic locus introgressed into another genetic background, and are one of the most powerful quantitative trait locus (QTL) mapping designs. However, albeit useful for QTL discovery, this homogenous background confounds genetic interactions. Here, we created a novel IL population, complementary to a previously created population, which enables identification of genetic interactions in ILs. The novel ILCB4856 panel was made by crossing divergent strains of the model nematode Caenorhabditis elegans (N2 and CB4856). The ILCB4856 panel comprises a population of 145 strains with sequencing confirmed N2 introgressions in a CB4856 background from which a core set of 87 strains covering the entire genome was selected. We present three experiments demonstrating the power of the complementary IL panels. First, we performed QTL mapping identifying new regions associated with lifespan. Second, the existence of opposite-effect loci regulating heat-stress survival is demonstrated. Third, by combining ILN2 and ILCB4856 strains, an interacting expression QTL was uncovered. In conclusion, the complementary IL panels are a unique and ready-to-use resource to identify, resolve, and refine complex trait architectures in C. elegans.