Abstract: The present study was conducted to quantify the effects of soil pollutants on soil inhabiting root-associated fungi. Roots of Parthenium hysterophorus (L.) subjected to fungal isolation revealed more diversity in fungal association compared to Desmostachya bipinnata (L.). Aspergillus was found most commonly associated fungi with the roots of both the plants. A total of seven different fungal species were isolated from the two plants. The root extracts of both the plants were found to have antibacterial agents. However, gram negative strains of bacteria were observed least sensitive. It seems that either plants or fungi, on polluted sites have co-adapted themselves in order to survive. Their interdependence is a manifestation of an association that cannot be strictly regarded as symbiotic but leads to an endorsing reciprocity.