Is this a conflict of interest for the CEO of both companies to be the same person, ( she is the CEO of the prime company and the CEO of the sub-contractor).
The mission of the Small Business Innovation Research (SBIR) program is to "...ensure that the nation's small, high-tech, innovative businesses are a significant part of the federal government's research and development efforts." Whether or not the prime contractor and subcontractor share the same CEO does not affect realization of this stated SBIR goal. Either way, a small business will receive an award in accordance with the intent of the SBIR program. FAR Part 2 defines conflict of interest as existing when "...a person is unable or potentially unable to render impartial assistance or advice to the Government, or the person's objectivity in performing the contract work is or might be otherwise impaired, or a person has an unfair competitive advantage."
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None of the three conditions stated in the definition appear to apply in your acquisition situation. The important issue is whether participation of the subcontractor as a small business meets the regulatory requirements for an award under the SBIR program. I recommend you consult with your organization's legal counsel for a more definitive response.