The research work focused on the interaction of plant and microbes. Initially investigation has been done in the area of role of Trichoderma in abiotic biotic stress tolerance and stress amelioration in plants. The work extended with exploring of microbes for the nanosynthsis of metal nanoparticles and its application in biodegradation, antimicrobial activity against MDR bacteria and phytopathogens. Along with this we have also studied the novel microsatellite markers for Trichoderma and Aspergillus species in order to elucidate whether it is possible to increase the resolution of existing markers to discriminate between individual strains or whether saturation of discrimination has been reached. This information is of fundamental importance when using microsatellites in future studies on the pathogenicity, ecology, or taxonomy of these species. In Trichoderma, twelve polymorphic markers were developed out of which six were from T. atroviride and remaining six belong to T. harzianum. Similarly, for Aspergillus species, we have developed five polymorphic markers for A. terreus and similar number of markers was developed for A. niger