Barnes & Noble (NYSE:BKS) is a company in crisis. Large losses suffered at its NOOK division have weighed on the bottom line, and its last two earnings reports were disastrous. But even the retail operation could be in peril. The company's founder and chairman, Leonard Riggio, announced that he would be abandoning his efforts to acquire it.

No doubt, Amazon (NASDAQ:AMZN) is responsible for much of Barnes & Noble's woes. From the beginning, the online retailer was built around selling books over the Internet; the introduction of the Kindle and the shift to digital only enhanced Amazon's dominance. But now the company is planning a hybrid of the two. By mixing digital with paper, Amazon could doom Barnes & Noble once and for all.

A big discount
Starting in October, Amazon customers who buy paper books from the retailer will have the option to buy a digital copy at a steep discount -- $1-$3, and in some cases, for free. This program, dubbed Kindle MatchBook, will even include books that have been purchased from Amazon in the past.

Not all books will fall under the program. At present, only 10,000 titles are included. Still, Amazon says it will work to expand the program to other publishers, and it seems likely that many of them will eventually sign on. The ability to squeeze an extra $3 out of most customers could prove enticing.

If Amazon didn't already have a competitive advantage, it definitely does now. Why buy a paper book from Barnes & Noble when Amazon bundles a cheap digital copy? Even if the book in question isn't currently part of the program, its potential to be added in the future could sway many customers.

To be fair, Barnes & Noble could copy the program with something of its own. But given that its NOOK division is already struggling, and there's talk that Barnes & Noble could spin it off or sell it to Microsoft, that seems unlikely.

Amazon's advantage over digital competitors
Amazon and Barnes & Noble aren't the only companies that sell digital books. In fact, Apple (NASDAQ:AAPL) might sell as many e-books as Barnes & Noble. Unfortunately, there are no hard market share numbers, but based on the Justice Department's recent e-book price-fixing lawsuit, Apple's share of the e-book market might be 20%.

If Amazon's market share is near 55%, a figure from Bowker Market Research, Barnes & Noble's is -- at most -- 25%, and likely much less, given that there are other players in the space, including Google.

Amazon's ability, then, to bundle paper with digital gives it as much of an advantage over Apple as it does over Barnes & Noble. Sure, many readers may have made the switch wholly to digital (including myself), but there are undoubtedly some readers out there who would like the flexibility of having both the print and digital versions of a book.

Apple isn't likely to start selling paper books anytime soon, so it'll never be able to match Amazon in this area.

Admittedly, iBooks aren't a big part of Apple's business. In fact, iTunes as a whole is largely insignificant when it comes to Apple's earnings. But that isn't to say that they aren't important. Media sales help keep customers locked into Apple's ecosystem, making them incredibly loyal. Someone who has bought a lot of iBooks isn't likely to give up the iPad -- to do so would be lose access to the digital books they've purchased.

Amazon continues its dominance of the book business
By combining paper book sales with digital copies, Amazon has a huge competitive advantage over its rivals.

Barnes & Noble, already in a precarious state, is heavily exposed. Right now, there are few reasons for book buyers to pick Barnes & Noble over Amazon; Kindle MatchBook makes it only more likely that consumers will go with the Internet retailer. At the same time, Apple may lose out on some iBook customers. To be sure, that won't turn up in the company's bottom line overnight, but it does weaken Apple's iOS ecosystem over the longer term.

Today, $0.31 of every $1 spent on books goes to Amazon. With Kindle MatchBook, that figure should only increase.

Sam Mattera has no position in any stocks mentioned. The Motley Fool recommends, Apple, and Google. The Motley Fool owns shares of, Apple, Google, and Microsoft. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.