Prothrombin is a serine protease precursor of the blood coagulation system. In this study, the primary structure of prothrombin of a cartilaginous fish, bullhead shark (Heterodontus japonicus), was determined using RNA-Seq and the protein was purified from the blood plasma. Bullhead shark prothrombin was found to be comprised of four domains, as in the case of reported mammalian homologues. Two arginine residues that should be cleaved by activated factor X were found in the amino acid sequence of the shark prothrombin, but only one of the two cleavage sites for thrombin or meizothrombin was conserved. The apparent molecular mass of the shark prothrombin on SDS-PAGE was 110 kDa, whereas that of its amino acid sequence was 65 kDa. Potential N-glycosylation sites were found at 79th, 108th, 121st, 179th, 199th, 507th, and 527th asparagine residues in the shark prothrombin, and treatment with N-glycosidase reduced the molecular mass to 65 kDa. This indicates that, in contrast to human prothrombin, which has only 7-kDa N-glycans, the prothrombin of the shark is highly N-glycosylated. This study is the first to report on the purification and characterization of blood coagulation factors in a cartilaginous fish.