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Well, at the end of the day and after weeks of speculation, Yahoo didn’t go with a former Microsoft or exec for the CEO post. Instead, the struggling Silicon Valley search and media company picked a guy with ties to PayPal.

Yahoo today announced that it has named Scott Thompson as CEO. The former president of PayPal, the online payments division of eBay, starts January 9th. Interim CEO Tim Morse will revert to his role as CFO of Yahoo.

“Scott brings to Yahoo! a proven record of building on a solid foundation of existing assets and resources to reignite innovation and drive growth, precisely the formula we need at Yahoo,” said Chairman Roy Bostock in a statement. “His deep understanding of online businesses combined with his team building and operational capabilities will restore the energy, focus, and momentum necessary to grow the core business and deliver increased value for our shareholders.”

Yahoo’s stock lost two percent on the news, continuing a slide for the one time tech titan. Thompson inherits one of the toughest job in tech, trying to reposition Yahoo as it has lost market share to rivals such as Google.

As part of the transformation, Bostock said that Yahoo is considering a wide range of opportunities, including “specific investments or dispositions of assets.” Reports have surfaced that Yahoo is looking to sell its Asian assets.

The company also has outsourced much of its search advertising business to Microsoft through a partnership announced several years ago. More recently, Microsoft, along with private equity backers, have been discussed as possible investors in the company.

Kara Swisher at All Things D — who first reported the news last night — had speculated about several possible candidates for the Yahoo job, namely former aQuantive CEO and Microsoft VP Brian McAndrews; Hulu CEO Jason Kilar; and former Microsoft CFO Chris Liddell.

In a statement, Thompson said that Yahoo has a rich history and solid foundation to build on.

“Yahoo is an industry icon and I am very excited about the prospect of working with one of the great teams in the online world to deliver Yahoo’s next era of success,” he said.
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