How to find and delete duplicate bookmarks in Google Chrome?

SuperSorter is a nice Chrome extension that seems to do the job. It's still in beta, but the removal of duplicates seems to work just fine.

Have a look at these articles (at your own risk):

How to Detect and Delete Broken Bookmarks From Your Browser using AM Deadlink

Scan, Delete Duplicate Bookmarks in Chrome with Bookmark Sentry

Bookmark Sentry and Super Sorter both do work, BUT the chrome bookmarks API gives them a quota for changes and as of july 2012, neither extension catches the errors when they exceed their quota for deleting duplicate (or reordering in the case of super sorter) bookmarks.

You can let super sorter run in the background (enable auto mode) and it will do a bunch of retries over time, and that may work around the quota issues with a string of partial successes... My experience, though, has been that chrome sync keeps disconnecting my browser when i make too many changes.

So the issue is not just deleting the duplicate bookmarks, it's removing them from your synced chrome browser state, which is a bit more complicated because the sync algorithm doesn't like so much change all at once.