Within the large and varied discipline of environmental biotechnology, microbial ecology has an integral role; the two subjects are inherently linked. With many of the foundation processes of environmental biotechnology based on naturally occurring ones, it is no surprise that the concepts and tools of microbial ecology offer insights into many environmental biotechnology processes. Recent advancements in microbial ecological (molecular) tools especially in those involving the Next Gen Pyrosequencing tools have led to substantial improvement in our understanding of the structure and function of natural microbial communities. These advances in microbial ecology can inform on the development of novel environmental biotechnological processes which are crucial for the functioning of an emerging modern society that demands sustainable management of its resources. However, effective integration of these new tools and knowledge into existing curricula so that students build the needed foundation in microbial ecology for application through environmental biotechnology remains a challenge. This talk presents some interesting ideas on how to facilitate this integration of microbial ecology and Environmental Biotechnology. Recent course developments for environmental biotechnology from a number of universities will be presented and discussed.