Abstract: This review starts with a brief introduction on principles and methods of microbiological molecular ecology as well as their applications in soil remediation. In addition to the genetic information of soil microbial community，the use of microbial molecular ecological tools enables the monitoring of the growth and function of inoculant degrading microbials，as well as their interaction with the indigenous microorganisms. These information are of fundamental importance for the selection and screening of degradation microbial communities，the intensification of degradation process，and the evaluation of remediated soil. Application perspective of microbiological molecular ecology is also discussed.