Hazardous waste sites around the world result from the manufacturing, storage, use, or disposal of compounds such as petroleum hydrocarbons, nitroaromatics, organohalogens, pesticides, and metals. Traditional remediation options are expensive and environmentally invasive. In last two decades, bioremediation has emerged as a more suitable alternative, mainly for the remediation of large polluted sites. Endophytic bacteria and fungi have been the subject of considerable study to explore their potential for improving the remediation of polluted environments. In case of phytoremediation of inorganic pollutants, endophytic bacteria can reduce the phytotoxicity and increase the mobilization and accumulation of heavy metals in aboveground plant biomass. The competency of several endophytes to degrade organic pollutants and their resistance to heavy metals probably originates from their exposure to these compounds, when present in the plant/soil niche. A wide range of molecular techniques have been applied to illustrate the ecology, diversity, composition, and role of endophytes in bioremediation. Fingerprinting techniques such as terminal restriction fragment length polymorphism (T-RFLP), denaturing gradient gel electrophoresis (DGGE), real-time PCR, microarrays, and metagenomics are being used to characterize the metal-resistant and organic pollutant-degrading endophytes.