A novel fusion protein system employing the substrate-binding domain (SBD) of poly(hydroxyalkanoate) (PHA) depolymerase was developed for the specific immobilization of proteins on PHA microbeads, and was consequently used for immunoassays. The enhanced green fluorescent protein, red fluorescent protein, and severe acute respiratory syndrome coronavirus envelope protein were used as model proteins, and were selectively and functionally immobilized to the PHA microbeads by fusing them to the SBD. Using this PHA microbead system combined with SBD fusion technology, immunoassays could be successfully carried out.