Alpha-2 macroglobulin (α2M), a broad-spectrum protease inhibitor, exists widely in vertebrates and invertebrates, but little information is available to date regarding α2M in amphioxus, an animal bridging from invertebrates to vertebrates. Here we first show that the full α2M cDNA of Branchiostoma japonicum (Bjα2m) contained 5545 bp with an open reading frame of 4593 bp encoding signal sequence of 16 amino acid residues and a mature protein of 1514 residues. The calculated molecular mass and pI of mature Bjα2M were 164.2 kDa and 4.6 respectively. Bjα2m was mainly expressed in the hepatic caecum and hind-gut in a tissue-specific manner, contrasting to the primary expression of α2M in vertebrate liver. Following challenge with lipopolysaccharide (LPS), Bjα2m expression was significantly up-regulated (7-folds) at 8 h and then declined to the base line at 16 h. Taken together, it is suggested that Bjα2M is an immune-relevant molecule possibly involved in the acute phase response via the digestive organs.