A complement system operating via the alternative pathway (AP) similar to that of vertebrates has been demonstrated in the primitive chordate amphioxus. However, the factor B (Bf), a key specific protease in the AP, remains elusive in amphioxus to date. We demonstrate in this study the presence of a factor B-like protein in amphioxus Branchiostoma belcheri by both immunoblotting and molecular cloning. The factor B-like protein was immunohistochemically localized in the hepatic cecum. The B. belcheri factor B-like gene, BbBf/C2, encoded a mosaic protein with three complement control protein (CCP) domains, a von Willebrand factor A (vWFA) domain and a serine protease (SP) domain. Peculiarly, BbBf/C2 had an epidermal growth factor-like domain (EGF_CA) located between CCP1 and CCP2, therefore BbBf/C2 had a modular structure of CCP-EGF_CA-CCP-CCP-vWFA-SP, making it a novel member of Bf/C2 family proteins. Real-time PCR assay revealed that lipopolysaccharide (LPS) challenge resulted in a quick and continuously significant up-regulation of BbBf/C2 expression in the hepatic cecum, while BbBf/C2 was only expressed for a short time in the hind-gut following LPS challenge though the expression level was temporarily higher than that in the hepatic cecum. Similarly, immuno-dot blotting showed that challenge with LPS triggered a significant elevation of BbBf/C2 synthesis in the hepatic cecum and hind-gut, with a higher rise in the former tissue. These results indicate that both hepatic cecum and hind-gut may be involved in the immune response induced by LPS, but the hepatic cecum, like the vertebrate liver, is the primary tissue synthesizing BbBf/C2 in response to LPS challenge, thereby playing a major role in the acute phase response.