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$44 million for Mr. Genius Bar

Another big payday for Apple’s senior vice president for retail

Johnson in 2009 at the opening of NYC's third Apple Store

Ron Johnson, the man Steve Jobs hired from Target (TGT) to create the Apple Store — and who famously persuaded his boss, over Jobs’ initial objections, to include a Genius Bar — has joined the string of top Apple (AAPL) executives taking advantage of the stock’s recent run-up to cash in some options.

According to an SEC Form 4 filed Saturday, Johnson sold 150,000 shares with a strike price of $11.06 on Thursday for an average price of $306.07, clearing $44,151,000 profit on the trade.

It’s the third big windfall for Johnson in the space of three years. On Oct. 31, 2007 — Halloween — he sold 700,000 shares with a strike price of $23.72 for just over $185 each, making $112 million on that deal. Then last March he sold another 200,000 shares, clearing nearly $46 million.

He still holds 232,875 “beneficially owned” shares, according to the latest Form 4.

Not that Apple’s decision to hire Johnson and reward him richly hasn’t paid off. Johnson now runs a chain of 317 increasingly expansive stores that generate more sales per square foot than Tiffany and have become, as Needham’s Charlie Wolf put it in a note to clients Thursday, “the face of Apple.”

In the company’s most recent quarter, revenues from the stores reached $3.57 billion, up 74% from last year.

“To place this number in perspective,” Wolf wrote, “Apple Store revenues in September were greater than Apple’s total revenues in every quarter in the company’s history until the third quarter of fiscal 2005.

“The Apple Stores continue to play a vital role in building the Apple brand,” he continues. “Through their array of post-sale services, the stores have become a magnet in attracting Windows users to the Mac platform. In the September quarter, Windows users purchased half of the 874,000 Macs sold in the stores. This represented 22% of the estimated number of Windows users who switched to a Mac during the quarter.”

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[Follow Philip Elmer-DeWitt on Twitter @philiped]