MNG described the moves as a "management realignment."
Today's announcement said that Wilson, 54, of Berkeley, will be "leaving the newspaper to pursue other opportunities."
Wilson had been executive editor of the IJ from 2004 until 2008 when he was promoted to publisher. He spent 22 years at the San Francisco Chronicle, serving as managing editor, executive editor, associate publisher and executive vice president for news.
Before that he was vice president of circulation for the Contra Costa Times for more than seven years and had financial and operational responsibility for several East Bay newspapers, including the West County Times, the Valley Times, the Antioch Ledger and the San Ramon Valley Times.
UPDATE, 5:10 P.M., JAN. 28: Mac Tully will be replacing Rounds as publisher of the Contra Costa Times, Oakland Tribune and other East Bay papers operated by MediaNews Group, those papers reported Friday afternoon.
Tully had been overseeing Rounds as publisher of the East Bay papers before the move. The newspaper group said it hopes the moves will help it operate more efficiently.
"We are trying to combine and utilize resources in the best way we can," Tully said.