New authors ask this question quite a lot. The short answer is yes; you need a separate ISBN for each different format of your book — paperback, hardbound, ePub, iTunes, etc. The exception is when you submit a book to Amazon/KDP; they use .mobi format, and assign their own numbering system to it, so a separate ISBN is not needed there.
For details, check out this really good article from Bookcoaching.com; it references the specific guidelines from Bowker (the authority and place you go to buy ISBNs) and explains it all pretty well.