Q: iBooks has suddenly stopped syncing between my iPhone and iPad

Didn't work for me.

Ditto here. I'd turned iCloud on and off during my conference with AppleCare. Glad it worked for Tony, though.

I tried many things, and it worked for one book between my iPad, iPhone and Mac, but it stopped.

I tried to log out to AppStore on iOS devices, and logout from the iBook Store on Mac,

I restarted devices, then log back in.

I removed all books and PDF from iCloud

I removed all download books

Nothing seems to solve the issue so far... In fact it's not an iCloud Problem, because the PDF I place on iBooks on the Mac are sync with my iOS devices.

The Bookmarks, Pages, Notes etc you edit in a book are sync with the AppStore, not iCloud...

I've found!

It's an issue from the app itself whether it's on Mac or iOS.

To Force Sync the notes, bookmarks and the page you were at:

- For example, if you're reading a book on the iPad, when you're done, close the app without closing the book.

- Force quit iBooks

- Open the book on the iPhone or Mac

- It should have sync

Let me know

Just fixed it after reading many posts here!  I have an iPad Air & iPhone 6s updated to 9.3.1 and my iBooks bookmarks were not picking up to continue reading after changing devices.  This fixed it:  Close iBooks on both devices.  On each device:  Settings, iBooks, Sync Bookmarks and Notes--Toggle off and back on.  Then reopen iBooks.  I opened iBooks on iPad Air first (don't know if the order mattered or not, but that was the last place I was reading), and it brought up the book I had been reading at the bookmark where I had stopped last night.  Then I opened iBooks on iPhone 6s.  Lo and behold!  My book opened right at the bookmark, exactly as it was supposed to do!!!  YAY!  Hope this works for you, too!

I'm glad it worked for you; unfortunately, it didn't work for me. My iPad and iPhone are still not syncing to each other. Thanks for trying, though!

I had done this on Thursday evening, but I tried again after reading your post. No luck for me. I do have to say, though, that my former iPad Air (now gone to live with my daughter and her family) didn't have the problem; it's only been since getting my new iPad Pro (smaller size) that this has been the case. Like you, I have an iPhone 6s.

Does this problem occurs on iOS 9.2?

To know if it's a software issue or Apple's server...

I think nothing will solve this issue for good, if the problem is from Apple

I didn't have the problem on 9.2. However, I also had an iPad Air (first version) with that. Now I have the new -- smaller --  iPad Pro, so there is an additional change to take into account in my case.

I created some collections on my mac and they still haven't showed up on my phone and tablet.

I also had this weird experience where I would read a book leave the app maybe close it. Go back open up the book and I had lost my spot and was on the first page of the book.

Any suggestions for that?

I'M having the same issue, and have been for several days. I've tried all of the fixes suggested (logging in and, force quitting ibooks, toggling the sync settings on and off, adding ibooks to iCloud, removing iBooks from iCloud, updating, restarting, etc) with no change. This is a huge pain in the neck, I'm hoping Apple fixes the problem soon.

I'm still on 9.2 and I can't sync any of my books at all, let alone bookmarks. I tried to put some new ones on last night and now I don't have any on my ipad mini except the books purchased through iBooks. I'm just downloading and updating to 9.3 now to see if that makes any difference.

Same problem here. Books sync but i can't sync bookmarks,position or notes.

Running iOS 9.1.3 and latest OS X as well.

Just to update: I installed 9.3 and I'm not sure what happened, but all my books are now back on my iPad. I did toggle the syncing option so that might have been it. I'm just afraid to ever try to add another book to it now after that.

I am having the same problem and I believe this happened after the 9.3.1 update. Very frustrating to hear that some have workaround and same workaround is not working for some. Hopefully, Apple figures this one out.  I am beginning to notice ever since Steve Jobs died Apple is becoming unreliable with their updates. I remember having to reset my devices when I upgraded to iOS 9.0 because it will not sense my backup on iTunes. I have been with Apple since iOS 6.x and all were good up to recently that I have noticed more and more problems with new iOS updates. I will HATE for this to be a TREND. Please Apple Engineers WAKE UP you are ruining a good thing!!!