CSIRO board chair Simon McKeon said his "wealth of experience in developing and applying science and technology makes him an excellent fit".
"The chief executive of CSIRO is probably the most important position in national science administration, so we conducted an extensive global search for an innovative scientist with strong business leadership qualities, and more than 70 candidates were considered," he said.
"Dr Marshall combines commercial and scientific credentials with extensive global experience, making him the world class leader we were seeking for CSIRO."
The physicist has 25 years experience as an international technology entrepreneur and is currently managing director of Southern Cross Venture Partners, a Silicon Valley based early stage venture capital firm specialising in creating Australian technology companies and growing them globally in Asia and the US.
He holds 20 patents protecting commercial products and has founded six successful US companies in biotechnology, photonics, telecommunications and semiconductors. They include Light Solutions, Translucent, AOC, Iridex (Nasdaq:IRIX) and Arasor (ASX: ARR), driving two of them to successful IPOs.
He will join CSIRO in January following Dr Clark's departure after six years in the top job. McKeon in particular pointed to her role in establishing research precincts and "major knowledge infrastructure projects such as the new research vessel".