The Chief Operating Officer and Chief Financial Officer of the online shoe retailer, Zappos, is leaving the company. Alfred Lin disclosed his plans to join venture capital firm Sequoia Capital in an email sent to all Zappos employees (which TechCrunch published.) In another email, Zappos chief executive Tony Hsieh denied rumors of the other two top executives leaving the company, as well.

A Zappos spokesperson confirmed the news, even though the company didn’t mean to release the emails publicly. The emails were leaked to the press, but Zappos says “it’s fine.” Zappos had no further comment, nor did Sequoia Capital reply to a request for comment.

Lin, who joined Zappos in 2006, wrote in his email that he was leaving the company mostly for personal reasons.

Lin writes,

First, Rebecca (my wife and my true boss) and I are getting into the baby business. :) [—] Over the past 2 months, Rebecca and I have talked a lot more about what is important to us and what we should do as a family. It is the general stuff you talk about, but you may only talk about superficially until it hits you that you are actually going to be a parent. As agonizing as it is for us to come to this conclusion, we really believe that the right place for us as a family is to move back to the SF Bay Area and be closer to some of our extended family.

Lin also says his true passion is being a venture capitalist, helping entrepreneurs build businesses around their visions and dreams. According to Lin, he actually “explored” joining Sequoia Capital twice, but it never happened.

Lin should be a considerable asset to Sequoia Capital. A Stanford drop-out, Lin was involved in LinkExchange back in 1996, which was later acquired by Microsoft for $265 million. Lin co-founded a venture fund called Venture Frog, which invested in many successful companies such as Zappos, Ask Jeeves, TellMe, MyAble and OpenTable, which have all been acquired or gone public. Lin joined TellMe, which was also acquired by Microsoft for $800 million. Then, Lin joined Zappos as COO and CFO, and saw acquire the company in July 2009. The price? Close to a billion dollars.

Lin is expecting to leave Zappos on January 3, 2011, but he says timelines may change and the transition “may be completed sooner.”

Tony Hsieh assured Zappos employees after Lin’s email that neither he nor Fred Mossler are going anywhere. Hsieh also put in a bit of a cliffhanger, saying in his email the two executives are working on a “secret long-term project”, which will be “really really cool and amazing for Zappos.” No further details were disclosed in the email.

Zappos gross merchandise sales exceeded a billion dollars in 2008.

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