Q: iBooks on IOS 9.3.1will not syncing between my iPhone and iPad

Try to reset your device. This won't delete your data stored on this device.

• Press and hold the Sleep/Wake button
• Press and hold on the Home button
• Keep holding both buttons until the display turns off and back on with Apple logo on it.

Alternatively, you may go to Settings - General - Reset - Reset All Settings

If this does not help, restore your device to factory settings. Note that this will erase the data from your device.

Take a look this Apple Support article: Use iTunes to restore your iPhone, iPad, or iPod to factory settings - Apple Support.

I've been having the same issue on my iPhone, iPad, and iMac for the last several days. Based on the other threads that have been posted about this, it seems to be a bug that was introduced with iOS 9.3 and remains unresolved in iOS 9.3.1.

I've tried a number of fixes including resetting my device, logging in/out of iCloud/iTunes, toggling "Sync Bookmarks and Notes," and so on. For me, the only thing that seems to have an effect is toggling "Settings > iCloud > iCloud Drive" from On > Off. That seems to force a single refresh of the bookmarks/notes, but it doesn't fix the problem.

I hope Apple fixes this soon. I filed a support ticket but I haven't heard back from them yet.

ce the iOS 9.3 update (I'm on iOS 9.3.1 now) notes, annotations, bookmarks, etc made on my iPhone, iPad or iMac do not sync with iCloud and with the other Apple devices.

this is a very important feature.

i Have signed out and back into iTunes, iCloud and rebooted each device with no effect or improvement. I have tuned "Bookmarks Syncing" off and on in iBooks with no effect.

I Am experiencing the same issue. As a beta user the syncing feature worked great. Every time I used iBooks all was synced between my devices. Since the final release of 9.3 and 9.3.1 I cannot get my bookmarks or reading place synced. I am now using Google Play Books across my iOS devices. Apple really dropped the ball on this.

I've read through this whole stream since I'm having the same issues. I walked through every workaround with a Senior Advisor but the problem was not fixed. He referred it to "Engineering" who in turned asked me to jump through ridiculous hoops. They asked me for things like (1) screenshot showing the current Settings > iBooks > and Settings > iCloud > iCloud Drive > screens [these were all verified on the phone with the Senior Advisor], (2) screenshot of the book on both devices with the bookmark inserted on one vs the other [Seriously? My word (as well as the Senior Advisor) isn't good enough, and a picture makes a difference?!?] and (3) the name of the book that you are currently experiencing this issue on [I established this was a global issue with all my book]. So, I call this, "The Apple Shuffle". Clearly, they are having an issue with the new iOS update and instead of acknowledging this, they run customers in nightmarish circles. I went through this with iTunes at one point and gave up only to find that one day, there is the new update, and viola, no more problem. Given the thousands and thousands of dollars I have spent on music and books (literally), this is a huge disappointment. How about good old honesty and ownership, like, "We have an issue and it will take a little time; please bear with us". Sad.

I have the exact same issue on our devices (ipad mini, iphone 6+). Wife has same setup and is experiencing the same problems. We had a ton of ebooks that we would sync notes, highlights, underline etc.between ibooks on both iphone and ipad. Worked perfectly fine until 9.3.1 )-: not cool. I have tried everything to test with no good results. Even tried new icloud sync feature, that seems to sync the files but does not sync content. HELP APPLE!!!

Im having the same issue with an iPhone 6s Plus and iPad mini, both up to date. Solutions listed above didn't work.

I have an iPod touch (4th gen, running iOS) and iPad mini (1st gen, running iOS 9.3.1). Before updating to iOS 9.3.1, I never had any problems syncing my epubs (bookmarks and highlighting). I have had all the versions of iOS running in my iPad mini (from iOS 7 through iOS 9.3.1), and this is the first time I have ever had a problem with iBooks. Please, we need help!

TThis problem is fixed in IOS 9.3.2 Public version that was released late this week.

I think that is my point. If this problem is fixed in 9.3.2 (a beta?) THEN why doesn't Apple just say there is an issue, and a fix is on the way. Instead, they told me they have not heard from anyone else on this problem but me, and wanted me (in addition to the lengthy service call I had) to take extraordinary, time-consuming steps to diagnose the issue. I don't understand such a deceptive maneuver. If someone can enlighten me as to why they do this, I would sure like to know. In the meanwhile, thank you "dfromwindsor junction". Do you know when 9.3.2 will be available?

NOt sure about the Apple philosophy on this, but happily it will be fixed.  Not sure when the official release will happen, but anyone can download the public beta For iOS 9.3.2

Thank you, "dfromwindsor junction". Odd, my books started synchronizing today, and I've done nothing different. Things that make you go, "Hmmmm".

I was notified yesterday by a senior support rep that Apple fixed this issue. Requires a restart on all devices. Works great for me now! No update needed on your devices.