Rapid industrialization and urbanization have generated huge amount of environmental pollution. Especially, synthetic organic chemicals have been a serious international problem for over half a century due to their toxic and hazardous chemicals. Eco-friendly strategies for removing the chemicals from the soil and water are becoming a top priority around the world and biological treatment such as phytoremediation and bioremediation is less expensive and more sustainable than other conventional remediation techniques. Recently, many pollutant diminishing microbial endophytes have been discovered from various plants grown in contaminated area and the function of microbes to improve phytoremediation of organic pollutants has been reported. Thus, we classify synthetic organic pollutants into groups of similar compounds and discuss the contribution of endophytes to enhance phytoremediation.