According to Apple, iBooks has an ability to sync bookmarks between iDevices over Wi-Fi. Suppose you are reading a book through iBooks on your iPhone and have some of its bookmarks, highlights and notes, now those will automatically get sync on iPad and iPod Touch as well.
By default, Bookmark syncing is disabled on iDevices, so first you have to turn it ON to make it working, so steps below will help you out to do that.
Sync iBooks Bookmarks to iPhone, iPod Touch and iPad
Tap on “Settings” icon on Springboard
Scroll down to “iBooks” and tap on it
Position the slider towards ON for “Sync bookmarks”
Note: To sync iBooks bookmarks you must have an Apple ID and your iDevice should be connected to Wi-Fi or mobile data service.