Dave McKinney was the Chicago Sun-Times' Springfield bureau chief.
He wrote a letter Wednesday to the CEO of Sun-Times' parent company, Wrapports LLC. It says he resigned because he believes the owners improperly influenced newsroom decisions.
The incident stems from a story McKinney co-wrote about a lawsuit alleging Rauner threatened a former employee.
Rauner's campaign called the story "irresponsible." It asked the Sun-Times to acknowledge that McKinney's wife is a Democratic media consultant "in the interest of transparency."
McKinney denies the conflict claim and the newspaper's editor publicly backed him after a "review."
Rauner is a former investor in parent company Wrapports.