The VC at the center of an Android vs. iOS debate bet publicly against Apple two years ago

“I am selling my entire position in Apple this morning including the stock I bought earlier than last fall. My average price on my entire position in Apple is $96, so I’ll take a small loss on this and a small gain on the stock I bought during the meltdown last fall.”

So wrote Fred Wilson, the managing partner of Union Square Ventures, in his widely read blog A VC, on Jan. 7, 2009. He had gone out to dinner with friends the night before and realized that none of them — “I mean nobody” — believed the statements coming out of Apple PR about Steve Jobs’ health.  “As good as the company is,” he wrote, “I just can’t own a stock when I don’t believe the company is being straight with investors.”

The story of Wilson’s decision to dump his Apple (AAPL) shares 27 months ago came up again this week because of two prominent blog posts he has written over the past six months advising app developers to write for Google’s (GOOG) Android in preference to Apple’s iOS.

“As I’ve been saying for several years now,” he wrote last Saturday, “I believe the mobile OS market will play out very similarly to Windows and Macintosh, with Android in the role of Windows. And so if you want to be in front of the largest number of users, you need to be on Android.”

That’s a controversial position, one that by Wednesday had generated nearly 600 comments — more than any other post in the history of his blog.

It has also prompted some critics to look back at Wilson’s 2009 AAPL liquidation and see how it worked out for him. At the close of market Thursday, Apple was trading for $338.08, which means the shares he sold for $91.36 on Jan. 7, 2009 have since increased in value $246.72 (270%).

Daring Fireball John Gruber, who has described Wilson’s Android posts as “terrible advice” for developers, was chortling about that stock trade on his Talk Show podcast Wednesday:

“So, you know, take your Apple advice from Fred Wilson with care.”

Wilson responded in the comment stream:

“I don’t regret my decision to sell $aapl.

“When I think the company is misleading investors, I don’t want to be a shareholder, no matter how much appreciation there might be in the future.

“And you should take a rabid fan like Gruber’s advice just as carefully as a rabid naysayer.”

For the record, Wilson also announced on Jan. 7, 2009 that he was selling his Google shares and holding on to Amazon (AMZN). Two weeks later he wrote that he was looking for an opportunity to buy back into Google, but not Apple. Since 1/7/2009 Google shares are up $250 (76%) and Amazon up $128.71 (229%).