Endophytic bacteria reside in plant hosts without causing disease symptom. In this study, 122 endophytic bacteria strains isolated from healthy oilseed rape plant were categorized preliminarily to 35 groups based on colony morphology; 16S rDNAs were amplified with universal primers of bacteria, all the strains could produce a single band about 1500bp, the PCR products were digested with restriction endoenzyme Hae III and Msp I respectively, different patterns were obtained for each enzyme, by combining all the restriction patterns for the two enzymes, the 122 strains could be grouped into 39 16S rDNA genotypes. The results indicated that endophytic bacteria from Brassica napus were genetically diversity. By comparing two methods, colony morphology only showed limited and preliminary information, and PCR-RFLP could be as a rapid and accurate tool for the diversity analysis of endophytic bacteria from Brassica napus.