Neelan Choksi, formerly the chief executive of e-book startup Lexcycle, announced today that he’s leaving Amazon, which acquired Lexcycle a year ago.

The startup created Stanza, which is still one of the most popular reading applications for the iPhone. Amazon has a Kindle iPhone app, but the two products seem complementary, since Stanza is a standalone product, not an extension of Amazon’s e-reading device.

Choksi just sent out an email announcing his departure. It doesn’t say much about why he’s leaving or where he’s going from here. His LinkedIn profile notes that he was moved off leading the Stanza team to a business development role at the beginning of the year, so that may be related. When I emailed Choksi for more details, he replied that he hasn’t made any decisions yet about what he’ll be working on next.

Here’s the intro:

I have decided to terminate my employment with Amazon. Today will be my last day. It saddens me that by doing so, I will also end my formal relationship with Stanza, and that I won’t be working with [Lexcycle cofounders] Marc [Prud’hommeaux] and Abe [White]. Both are truly gifted technologists, and I have been spoiled getting to work with them through 5 companies over the past decade. I have a tremendous amount of passion for Stanza and am truly sad to no longer be working on a project that has had such an amazing effect on an industry and for our nearly 4 million users worldwide. This decision did not come easily.

Don’t miss MobileBeat 2010, VentureBeat’s conference on the future of mobile. The theme: “The year of the superphone and who will profit.” Now expanded to two days, MobileBeat 2010 will take place on July 12-13 at The Palace Hotel in San Francisco. Early-bird pricing is available until May 15. For complete conference details, or to apply for the MobileBeat Startup Competition, click here.