We developed a method to identify serological humoral immunodominant proteinic antigen of Mycoplasma hyopneumoniae (Mhp). After constructing the recombinant plasmid pGEX-6P-1-mhp366 and transforming it into Escherichia coli BL21(DE3), the recombinant GST-Mhp366 protein was expressed successfully. The lysates of the recombinant GST-Mhp366 and genetic engineering GST were added into glutathione coated plates and reacted with 17 positive sera or 13 negative sera. Meanwhile, the optimization of experimental conditions, including coated antigen, blocking buffer, dilutions of sera and second antibody were determined. The optimal concentration of the coated antigen was the original bacteria lysates without dilution, and the optimal blocking buffer contained 10% FBS and 2.5% skim milk in PBS. Besides, the working concentration of serum samples and the HRP-tagged rabbit anti-pig IgG secondary antibody were 1:500 and 1:40 000, respectively. Thus, an indirect ELISA was established for identification of immunodominant protein antigens of Mhp. Meanwhile, this method was confirmed by the identified serological humoral immunodominant proteinic antigen Mhp156 and Mhp364. This method can be used for identification of the candidate vaccine antigens on a genome-wide scale. Furthermore, it can lay the foundation for identifying the candidate vaccine antigens through colostra and the nasal mucosal secretions.