The present work was undertaken to study the genetic diversity among 25 native Rhizobium trifolii-clover isolates obtained from the Sohag governorate during 2020 from different locations. morphological markers of the isolated Rhizobium included gram stain; salinity tolerance and pH tolerance were evaluated.  At the same time, Biochemical markers included Catalase, Citrate utilization, Bromothymol blue, Lysine decarboxylase, and Lipase were tested. Tow of Molecular markers for this isolated Rhizobium included 16S rRNA, and SRAP marker was also studied. Isolates demonstrated a low similarity coefficient, which may reflect a higher diversity of Rhizobium trifolii isolates within the fields. A cluster analysis realized using Jaccard's coefficient for the data of SRAP markers, revealed similarity coefficient values ranging from 0.25 to 0.91. The UPGMA cluster analysis based on the SRAP markers according to the data of this work is in full harmony with the previous studies in which PCR genomic fingerprinting is an adequate technique for differentiating Rhizobium strains.