Answer: I prefer selling on Amazon because it is just so much more efficient than eBay (in most cases). You can list your books for sale much faster, and I believe they sell faster on Amazon because the buying process is so much simpler and easier for the buyers.
Another big plus in selling books on Amazon is that you can capture some sales from book buyers who go to Amazon, originally with the intention of buying a new book. They get to Amazon's site expecting to pay $20 for a new book, and notice that a used bookseller has the same thing they're looking for in excellent condition for only $10. So you get lots of sales on Amazon from people who hadn't even considered buying a used book.
However, there are some instances when I think it's good to sell on eBay. If you have a collection or assortment of one authors' books, you could sell it as a package. For example, if you had one copy of each book written by Stephen King, you could sell it as an "instant Stephen King collection" and it would surely receive lots of attention, and sell for more than you could get for each of the titles individually.
And there are lots of booksellers that believe if you have a truly unusual, collectible book, you can get a higher price by auctioning it on eBay than you can selling it at a fixed price on Amazon.
So even though I prefer selling on Amazon to eBay, I have active accounts on both sites because I don't want to put all my eggs in one basket. For example, what would happen if your whole business depended on Amazon, and one day Amazon decided they didn't want to allow independent sellers on their site anymore? In that case your whole business could go down the tubes. So I would recommend that sellers maintain an active eBay account, just to avoid becoming totally dependent on a certain sales venue.
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Steve Weber is author of "The Home-Based Bookstore: Start Your Own Business Selling Used Books on Amazon, eBay or Your Own Web Site" (ISBN 0977240606). Got a question for Steve? Send to: steve_weber@yahoo.com