This short review describes the molecular evolution and phylogeny of various defense molecules participating in the host defense of horseshoe crab. It is well known that invertebrate animals, which lack adaptive immune systems, have developed various defense systems, so called innate immunity, that respond to common antigens on the surface of potential pathogens. The systems include hemolymph coagulation, melanization, cell agglutination, antimicrobial action, active oxygen formation, and phagocytic action. Among them, hemolymph coagulation and phenoloxidase-mediated melanization, in addition to cell agglutination, are directly induced by foreign substances, that result in the engulfment of invading microbes. The immobilized invaders are finally killed by antimicrobial substances released mainly from many kinds of hemocytes. In the past two decades, we have investigated biochemically various defense molecules, using horseshoe crab as a model animal, and established extensively their molecular structures. These results now make it possible to discuss evolution and phylogeny of the defense molecules at a molecular level, in comparison with those derived from vertebrate animals. Here, the authors will describe the present state of our knowledge concerning molecules mainly associated with innate immunity.