Background Plant-endophyte partnership provides an excellent gateway toward restoration of contaminated ecosystems. The interactions between both partners can be manipulated by introducing novel catabolic/ metabolic genes into host plant or endophytic bacteria genomes. The potential of the engineered organisms to degrade or accumulate contaminants is much wider than their wild relatives. Scope This review covers the recent developments for engineering catabolic/metabolic genes from a wide range of sources into plants or endophytic bacteria for the development of modified plant-endophyte interactions. Genetic alteration of plants promises enhanced catabolism by plant's own enzymatic machinery or greater contaminant uptake/accumulation for subsequent in planta detoxification by complementary endophytes. On the other hand, bacteria may also be engineered to enhance the potential for degradation or alteration of catabolic pathways, either to protect the host plant against phytotoxicity or to improve the overall efficiency of phytoremediation in planta, a situation especially suitable when hydrophilic compounds fail to be degraded by rhizospheric microbes due to the rapid uptake by plants. This is followed by discussion on kinetic parameters controlling phytoremediation. Conclusions It is hypothesized that transgenic approach can result in synergistic and effective plant-endophyte partnerships for wider-range and enhanced capabilities of degrading and/or detoxifying contaminants.