The Book Industry Study Group has produced guidelines for assigning ISBNs to digital books. The committee consisted of major traditional publishers, university presses, Bowker, Ingrams, B&T. Here is a link to the pdf file of the policy:  http://www.bisg.org/docs/BISG_Policy_1101.pdf. You will want to note pages 5 & 6 in particular.

Basically, it has been decided that each format of digital book requires its own, single ISBN, regardless of how or where it is sold. Amazon assigns its own type of identifier, however it looks like a Kindle-format book should have its own ISBN anyway. This policy goes into effect March 2012.