As others have mentioned, generally beekeepers know what plants are nearby. If you know you have a lot of clover nearby, and your honey tastes like clover honey — well, you’ll probably label it clover honey.
Along those lines — plenty of folks just taste the honey and take their best guess. Not perfectly accurate, but it’s usually accurate-ish.
If you want to get nerdy about it and have the right equipment, you can actually look at individual pollen grains in the honey and figure out what plant they belong to. Or, you can even use DNA in some cases!
But generally it’s a matter of deductive reasoning. If your honey looks like a duck and quacks like a duck… or in this case, looks like clover honey and tastes like clover honey…. 🙂
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