Botulinum C₂ toxin (C2T) elaborated by certain strains of Clostridium botulinum types C and D is composed of separate and dissimilar two proteins, components I and II. Previous studies have shown that these two components of C2T produced by type C and D strains were immunologically heterologous and that C2T-producers were classified into three groups depending on the difference in molecular characteristics of the components I and II. In the present study, the heterologous component IIs of C2T were purified from three representative strains of the groups and the molecular characteristics of the components were compared. Immunological analyses by agar gel double immunodiffusion test showed that the component IIs purified from the three strains have the specific epitope(s) in addition to the common one(s). The biological activity of C2Ts reconstituted with component I purified from a fixed strain and component II each from the three strains differed depending on the source of the component II. These results indicate that the component II of C2T produced by C. botulinum types C and D differs in molecular structure, which reflects on the difference in the biological activity of the toxin. The present study suggests that the pathophysiological activity of C2T, which possibly causes a necrotic enteritis, is dependent on the C2T-producing bacteria infected.