A venture capital executive with ties to defunct solar company Solyndra has been hired as the new chief of the Defense Department program heading up the Pentagon’s renewable energy push.

Arati Prabhakar, a former partner at U.S. Venture Partners, a Silicon Valley-based venture capital firm that backed Solyndra, has been named the new director of DoD’s Defense Advanced Research Projects Agency (DARPA). Prabhakaker will administer DARPA’s roughly $3 billion budget, some of which will likely continue funding projects in renewable energy.

While there is no indication that Prabhakar was involved with Solyndra during her time at USVP, her appointment to DARPA may rekindle allegations of cronyism in the administration’s dealings with Solyndra and other green energy companies.

DARPA itself has been scrutinized for some of its green energy deals. Former chief Regina Dugan was investigated by federal watchdogs after her family’s company won $400,000 in DARPA contracts while she headed the division.

DARPA was also responsible for the $21.8 million deal with biofuel company Solazyme, inviting further scrutiny. A member of Solazyme’s corporate board sat on President Obama’s transition team, where he helped form renewable energy policy.

Given the large pricetag of the Solazyme deal – the Navy paid $26 per gallon for Solazyme fuels – its merits mention that Prabhakar stresses the importance of relying on alternative energy despite its admittedly high costs to American taxpayers.