title_body: Is there an ebook format that stores annotations in the ebook file itself? I believe .epub and .mobi files both don't support annotations. Which is unfortunate since they are some of the most popular formats. It looks like Kindle supports adding notes to ebooks but they are stored separately from the ebook file itself and I'm a big believer in 'the truth is in the file'. PDFs allow annotations but they don't reflow like most ebook file formats.
  
  This question is slightly different from the one I listed below in my comment because that question is asking about a note file format and I'm asking about an ebook file format.
upvoted_answer: Simple answer: NO
  
  To annotate inside an ebook would require the file to be altered on the device side and some sites will not allow this due to the DRM they add.  That said this is why Kindle creates a secondary file instead of in the ebook itself.  This would also depend on the app you are using to view the ebook on.  
  
  Some apps that allow Annotation for books:
  
  
  iAnnotate
  Subtext
  Mantano Ebook Reader
  iBooks
  Marvin