Arid and semi arid regions of the Indian Thar Desert possess several nodulating native legumes important to the local inhabitants for food, fodder, shelter and medicines. These legumes are useful in dry land Cultivation and soil improvement for rain-fed crops in arid and semi arid areas, The present study was aimed to characterize the genetic diversity of thirty one root nodule bacterial endophytes strains from Tephrosia purpurea and Tephrosia villosa growing in Jodhpur and surrounding districts of Rajasthan (India), These two plants are widely distributed in degraded and waste land in the arid and semi arid regions of many states of India