This book highlights the importance of molecular genomics and molecular biology techniques used to sort out the problems faced by industrialists who operate wastewater treatment plants with the ever-increasing number of environmental pollutants, through an approach of microbial community analysis. Current knowledge of the microbial communities within biological wastewater treatment reactors is incomplete due to limitations of traditional culture-based techniques and despite the emergence of recently applied physico-chemical and biological techniques. This book will give a complete overview about an advanced molecular technology for microbial community analysis of a wastewater treatment reactor to understand and gain proper knowledge, which may help to ultimately sort out the issue of environmental pollutants. It will give an insight about an application of various molecular tools to investigate microbial community composition or structure in activated sludge processes.