Amphioxus is an important animal model for phylogenetic analysis, including comparative immunology. Exploring the immune system in amphioxus contributes to our understanding of the origin and evolution of the vertebrate immune system. We investigated the amphioxus immune system using ultrastructural examination and in situ hybridization. The expression patterns of TLR1 (toll-like receptor 1), C1Q (complement component 1, q subcomponent), ECSIT (evolutionarily conserved signaling intermediate in Toll pathways), SoxC, DDAHa (Dimethylarginine dimethylaminohydrolase a), and NOS (nitric oxide synthase) show that these genes play key roles in amphioxus immunity. Our results suggest that the epidermis and alimentary canal epithelium may play important roles in immune defense, while macrophages located in the coelom and so-called lymph spaces may also be crucial immune cells.