Microbial DNA extracted from two soil samples collected from Beni-Suef and Kafr El-Sheikh were subjected to PCR amplification with primers specific for 16S rDNA gene and cloned in linear pCR 2.1 plasmid vector. Recombinants were transformed into Escherichia coli competent cells. Sixty clone inserts (30 from each soil sample) were sequenced and subjected to phylogenetic analyses. Forty sequences of the sixty clones were affiliated with previously recognized bacterial groups. Thirty six of these had closest relatives among cultured taxa and clustered primarily with three divisions containing microrganisms commonly associated with soil: Proteobacteria, Gram-positive organisms, and Cytophaga-Flexibacter-Bacteroides group. The results also showed the presence of one clone related to Nirospira retrieved from Beni-Suef soil, one clone from Archaea kingdom retrieved from Kafr El-Sheikh soil, and three clones affiliated to the newly described Holophaga-Acidobacterium phylum in both Beni- Suef and Kafr El-Sheikh soils. Seven sequences grouped with known divisions but had closest relatives among soil taxa known only from rDNA sequences analysis. Twelve clone sequences were distantly related to known sequences. Many of these sequences may represent new bacterial divisions.