This study investigates the rhizosphere effect exerted on the microbial communities by three rare endemic and threatened medicinal plant species of the Amarkantak region of Central India. Amarkantak region with its rich and varied biodiversity is natural habitat for various tribal communities. These tribal inhabitants use different plants for their basic necessities which have led to its indiscriminate exploitation. Some of these selected threatened and rare medicinal plants viz., Litsea glutinosa, Rubia cordifolia and Pueraria tuberosa of Amarkantak region require efforts for conservation and its propagation. A microbial community is considered to be an important factor for improving soil quality. Structure of soil bacterial communities not only differs in different habitats but also between rhizosphere and non-rhizosphere. Microbial population associated with these medicinal plants was examined with respect to colony forming unit and the rhizosphere:soil ratio. A positive R:S ratio was found and the total viable count of all the soil samples from different site range from 10 x 10³ to 132 x 10³.  The R:S ratio was found to range between 1.061 and 3.55 indicating positive rhizospheric effect. Out of 79 bacterial isolates, over seventy five percent of the isolates were found to be Gram negative rods.