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Skunks will scratch at the entrance of the hive to draw the bees out.  

They then consume the adult bees as they fly out of the hive. Typically this will happen at night and skunks can decimate a colony in no time at all. They also irritate the bees making them cranky and difficult to work. Look for signs of scratching on the hive and skunk feces with bee exoskeletons in it. There may also be mud and torn-up vegetation in front of the hive.

Raise your hive up, off the ground; higher is better. Skunks must then stand on their hind legs to reach the entrance exposing their tender underbelly to the stings of your colony. Another option is to take a piece of plywood and nail a lot of nails through it. Then place the wood, nails up, in front of the hive.