Characterization of a novel C1q-domain-containing protein of the Japanese flounder. PoC1ql3 was expressed not only in the brain, but also in many immune-related tissues. C1ql3-full and C1ql3-part protein exerted antimicrobial function against E. tarda in vitro. The C1ql3-part bound LPS and PGN as pattern-recognition receptor. The C1ql3-part inhibited the invasion of bacterium to fish kidney cells in vivo.