The integration of molecular biology tools in environmental engineering is a challenge. We discuss our views on the following four critical issues: (I) faculty career development, (II) tool standardization, (III) teaching, and (IV) the application of molecular biology tools in practice. For (I), we suggest that administrators and faculty need to understand the special challenges inherent to research and teaching within this highly interdisciplinary area. Furthermore, we suggest preparing two white papers aimed at educating administrators in universities and agencies. For (II), we conclude that, because molecular biology tools are still in a state of rapid development, proposing standards at this time is premature. In the future, standards for widely applied tools should be in an on-line, peer-reviewed format. Concerning (III), we believe that molecular biology should be taught only to the degree needed to achieve program goals. For example, environmental engineering practitioners only need to know the vocabulary and basic concepts of molecular biology tools, not be experts at doing them hands on. To help engineering students gain the right level and type of information, learning modules should be developed for them. Finally, although engineering successes applying molecular biology tools are available (IV), the biggest value will come when the tools are fully integrated with practice. Therefore, we encourage the creation of a demonstration project to document the value of applying molecular biology tools in environmental engineering.