In this work, we reported the role of RNase on microbial community analysis from soil samples. The amounts of chemical components were measured from the adjoining soil of rice and wheat plants. The chemical properties of these soils were rich in surface level as compared to other soil layers. Total DNA was extracted from freshly collected soils. To obtain pure DNA, half of the sample was incubated with RNase and half was without RNase. A total of 16S rDNA fragments were amplified and analyzed by Denaturing Gradient Gel Electrophoresis (DGGE). RNase-treated DNA followed by PCR resulted in a PCR product of good yield and integrity. DGGE bands and cluster analysis indicated a significant difference between the patterns obtained from RNase-treated and RNase non-treated samples. The sequencing results of 16S rDNA fragments from DGGE profiles of soil samples indicated that the dominant bacteria are composed of different gene sequences. This is an interesting preliminary observation which indicates that the RNase treatment prior to amplification and DGGE analysis modifies the pattern obtained. Therefore, it is suitable for community analysis of agricultural plant soil samples as well as environmental samples.