I've only recently just started using Safari, mainly to separate my personal accounts from my work accounts. As such, I've logged into Gmail in safari for one of my email accounts. I spent a while setting up bookmarks, configuring toolbars, etc.
I've just updated my MacBook Pro to 10.11.3, and suddenly Safari is showing all of my Chrome bookmarks, mixed in with the Safari ones I set up earlier.
I'm not logged into iCloud, I can't find anything in preferences to suggest syncing the bookmarks, and a quick google even leads me to suggest that it's not trivial to do so!