E-books and ISBN's remain a testing issue for many publishers. I have also come across a great deal of misunderstanding from authors who self-publish as well. A recent study paper by the International ISBN Agency reveals that they still stand by their 2005 recommendation that all electronic formats of a book should have a separately assigned ISBN.
From the study paper:
"Since its creation in the late 1960s the purpose of the ISBN has been to facilitate book supply chains which by their very nature will evolve and create new demands over time. In the digital environment, it has become less clear how supply chains will develop and, because of that, there has been uncertainty amongst some publishers of the role of ISBN in this market.
One of the principles of ISBN has been that it identifies a unique product (e.g. an edition of a book). This has facilitated discovery and acquisitions, and enabled e-commerce, distribution and aggregation of product information, and sales data reporting. The ISBN standard, ISO 2108, has always required that different product forms of a publication, where these are made separately available, be assigned separate ISBNs.
When the standard was revised in 2005, there was considerable discussion about the appropriate level of granularity for electronic publications. It was agreed that the same rules that had been applied to printed books should also apply to e-books and the current edition of the ISBN standard, ISO 2108:2005, therefore reads:
Each different format of an electronic publication (e.g. '.lit', '.pdf', '.html', '.pdb') that is published and made separately available shall be given a separate ISBN."
If you want to read the ISBN Agency Study Paper, then please click here.