WASHINGTON—Before the 2016 presidential election, a longtime Republican opposition researcher mounted an independent campaign to obtain emails he believed were stolen from Hillary Clinton’s private server, likely by Russian hackers.

In conversations with members of his circle and with others he tried to recruit to help him, the GOP operative, Peter W. Smith, implied he was working with retired Lt. Gen. Mike Flynn, at the time a senior adviser to then-candidate Donald Trump.

“He said, ‘I’m talking to Michael Flynn about this—if you find anything, can you let me know?’” said Eric York, a computer-security expert from Atlanta who searched hacker forums on Mr. Smith’s behalf for people who might have access to the emails.

Emails written by Mr. Smith and one of his associates show that his small group considered Mr. Flynn and his consulting company, Flynn Intel Group, to be allies in their quest.

What role, if any, Mr. Flynn may have played in Mr. Smith’s project is unclear. In an interview with The Wall Street Journal, Mr. Smith said he knew Mr. Flynn, but he never stated that Mr. Flynn was involved.

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A Trump campaign official said that Mr. Smith didn’t work for the campaign, and that if Mr. Flynn coordinated with him in any way, it would have been in his capacity as a private individual. The White House declined to comment.