As a publishing consultant, I often get asked about the mysterious ISBN, what it does, who needs one, and why.
Laura Dawson (Publishers Weekly) wrote an informative article about the International Standard Book Number — Hooray for the ISBN — and why it’s important to have one for each format of one’s book, including the Kindle (.mobi format).
Yes, I know Kindle/Amazon does not “require” an ISBN. That doesn’t mean you shouldn’t assign one that’s different from the .ePub format (the two formats are different technically, just as a paperback is different from a hardcover edition; thus, each one needs a separate ISBN).
It’s also important (IMHO) to own one’s ISBNs and get them directly from Bowker, rather than from another entity, such as CreateSpace or Smashwords.
Yes, ISBNs can be expensive when purchased one at a time, but I believe it’s a shortsighted decision to take the “free” ISBN. If you buy even as few as ten at a time, they are $25 each. I see it as a cost-effective business/marketing expense. Not only does it give you full control over the ISBN and the meta data associated with it, it gives you greater credibility and market visibility, as the linked article points out.