Abstract:Taking endophytic bacteria as experimental materials，electrophoresis analysis were performed by setting a single loading sample，repeated loading samples，different loading amount about sodium dodecyl sulfate -polyacrylamide gel electrophoresis（SDS-PAGE）of whole cell soluble protein，depending on the relative motilities of each standard protein to estimate the molecular weight range of protein subunits，combinating with 16S rDNA sequences to distinguish the relative molecular weight of different strains from soybean nodules to facilitate further research.The results showed that the protein bands of different strains were different，their genetic relationships were different，indicating more distant relatives.16S rDNA sequencing analyzed indicated strain 44 was the most similar genera Bacillus horikoshii，52 was the most similar to Sinorhizobium fredii，strain 70 was the most similar with Ochrobactrum intermedium；Repeated electrical samples suggested strains 7 and 53 had the same proteins profile，and the analysis of 16S rDNA sequences showed the most similar genera was Bacillus subtilis，and the most similar strain was HRA69，indicating they were the same species.Protein profiles of 123 and 125 combinated with 16S rDNA sequences and comparison，the most similar genera was Bacillus cereus.Electrophoresis results showed that different loading amount of same strain did not affect protein profiles，16S rDNA sequences results furtherly confirmed the most similarity was invariant，did not affect the genetic relationship.