This paper explores the dynamics of the configuration of the national, the sectoral and the technological innovation systems and defines the configuration of these three innovation systems as the national, sectoral and technological innovation systems (NSTISs). Through comparing the Taiwanese pharmaceutical biotechnology and agricultural biotechnology innovation systems we find that even within the same nation different NSTISs reveal different dynamics, in terms of actors and networks, the application of technology and knowledge and institutions. We conclude that the new research, technology, development and innovation policies should be customized according to the differing dynamics of the NSTISs. Copyright The Author 2012. Published by Oxford University Press. All rights reserved. For Permissions, please email: email@example.com, Oxford University Press.