Plant Microbe consortium developed efficient multistrategic biodegradative mechanism to cope with different toxic pollutants. Native plants with diverse applications and limited resources for large scale cultivation can ensure eco-friendly restoration of polluted areas. Genomic information generated through high sequencing technologies like illumine Hisequencing removed the constraints in tackling hidden non-pathogenic microbial population inside plant tissues. Endophytic microbial associations spurred phytoremediation as plant growth promotion activity. Metagenomic screening of bacterial endophytes from Emilia sonchifolia (Linn.) DC. disclosed the phytoremediation potential of both culturable and nonculturable endophytes with specific role in bioremediation. Gene annotations indicating the production of enzymes in degradative pathways of compounds like Chlorocyclohexane and chlorobenzene, Fluorobenzoate, Furfural, Dioxin, Xylene, Toluene, Polycyclic aromatic hydrocarbons, Chloroalkane and chloroalkene, Naphthalene, Aminobenzoate, Nitrotoluene, Ethylbenzene, Styrene, Atrazine, Caprolactam clearly emphasis the role of endophytes in phytoremediation potential of host plants.