This review summarizes literature demonstrating the application of molecular biology methods in biological systems with specific applications in biological waste treatment, public health, and bioremediation. This review also highlights new methods that were developed in 2004. Because different molecular methods have different limitations, environmental engineers and scientists need to use care in interpreting the results of experimental procedures. Notably, the quantitative limitations of some of the molecular methods must be understood and discussed. In addition, molecular biology methods offer powerful approaches for understanding the microbial communities in biological systems, but researchers and practitioners share the responsibility of translating this new knowledge into useful practical outcomes.