Building a European "Knowledge Based Bio-Economy" is a multidisciplinary process bringing together science, industry and other stakeholders, to exploit new and emerging research opportunities that address social, environmental and economic challenges. In the activity "Sustainable production and management of biological resources from land, forest, and aquatic environments" Systems Biology is part of the enabling and emerging technologies for developing new tools. Concerning the activity on "Fork to farm: Food (including seafood), health and well being" Systems Biology plays a role for understanding beneficial and harmful dietary factors. Finally, in the activity "Life sciences, biotechnology and bio-chemistry for sustainable non-food products and processes" Systems Biology is part of the emerging technologies (like bioinformatics, nano-biotechnology and synthetic biology), to enrich the biotechnological tools for the development of an industrial biotechnology, sustainable and friendly to the environment. Among these emerging technologies Synthetic Biology plays a prominent role by enabling a rational (engineering) recreation from basic elements of predetermined metabolic and catalytic properties. Synthetic biology may lead to minimal or even totally artificial microorganisms that can be used for microbial production processes with significant advantages in industrial or environmental biotechnology particularly where complex metabolic networks are required. It has become a platform of international discussions and debates on ethical, legal, safety and societal issues.