Origanum majorana L. commonly known as sweet marjoram has been used for variety of diseases in traditional medicine, including gastrointestinal, ocular, nasopharyngeal, respiratory, cardiac, rheumatologic, and neurological disorders. Protein gel electrophoresis is the commonly used technology to separate proteins according to their physical properties such as electrical charge and molecular weight.In present study, polyacrylamide gel electrophoresis (SDS-PAGE) was used for identification of marjoram plants treated with biocontrol agents collected from Egypt and studying the differentiation among them.SDS-PAGE was examined for plants treated with four biocontrol agents;Bacillus megaterium,Fusarium aquaeductuum,Trichoderma harzinum+Fusarium aquaeductuum and Bacillus megaterium+Trichoderma harzinum +Trichoderma hamatum+Fusarium aquaeductuum.Protein analysis revealed that, application of the biocontrol agents significantly increased protein bands than control or plants cultivated in the infested soil, best results were obtained when B. megaterium was applied.