Drawing upon the regional innovation systems (RIS) approach in the globalizing economy, the chapter examines the evolution of regional innovation systems in China, with special emphasis on emerging indigenous innovation in Shenzhen, China’s first Special Economic Zone located in the Pearl River Delta. The transformation of innovation policies in China is explored, particularly in the aftermath of the 2008 global financial crisis, through the development of state-designated strategic emerging industries and subsequent effects on the technological dynamisms in Shenzhen. Particular attention is paid to the emergence of indigenous innovation as regional innovation systems evolve. The chapter sheds light on the emerging paradigm shift of state innovation policy towards indigenous innovation with a focus on domestic firms. Notwithstanding this new focus, the empirical experience in Shenzhen indicates that indigenous innovation focused on domestic firms may unnecessarily exclude the participation of trans-national corporations.