A clip domain family of serine proteases has been identified in invertebrates as a crucial enzyme involved in diverse biological processes including immune responses and embryonic development. Although these proteins contain at least one clip domain at the N-terminal of the serine protease domain, the roles and three-dimensional structure of the clip domain are unknown. Prophenoloxidase activating factor-II (PPAF-II), a clip domain family of serine proteases, derived from the beetle Holotrichia diomphalia larvae, was overexpressed in the baculovirus system, and crystallized using the hanging-drop vapor-diffusion method. High-quality single crystals of PPAF-II were obtained in a precipitant solution containing 0.15 M ammonium sulfate, 1.25 M lithium sulfate monohydrate, and 0.1 M sodium citrate dehydrate (pH 5.5). These crystals belong to space group C2 with unit-cell parameters a=107.84, b=76.78, c=70.49 A and beta=113.93 degrees , and contain one or two molecules in the asymmetric unit. Determination of the three-dimensional structure of PPAF-II would clarify the functions of the clip domains.