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Were bookmarks previously sync'd over the cloud? If so, go to your settings and see if something is turned off. Make those changes and allow for another sync to take place. My bookmarks were wonky too and that is what I did.
 
All right, and if there aren't any bookmarks and you know your computer is still set up to sync to the cloud too, did you try a reboot? Next, I would re-sync (wifi) to iTunes and see if that helps matters.
 
All right, and if there aren't any bookmarks and you know your computer is still set up to sync to the cloud too, did you try a reboot? Next, I would re-sync (wifi) to iTunes and see if that helps matters.

Reboot of phone worked. All bookmarks are back. Weird that that hapened to begin with.
 
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