Honey Trees were first introduced in Pokémon Diamond, Pearl, and Platinum. Special trees allowed trainers to catch rare Pokémon that would otherwise not have been available. However, the feature was removed from subsequent Pokémon games for unknown reasons. That said, with the release of Pokémon Brilliant Diamond and Brilliant Pearl, the feature is back too, and here's how to use it.
How do honey trees work?
To use honey trees, trainers must smear them with honey, which is a consumable item in the game. Once you've smeared it with honey, head back to the tree after six hours and you'll be able to meet a special Pokémon. However, if you don't commit to Honey Tree for 24 hours after smearing it with Honey, you won't encounter a Pokémon and lose Honey. Please note that the meeting is not guaranteed after six hours and you must continue to check periodically until the 24 hour mark. When you see that the tree is shaking, it indicates that there are wild Pokémon ready for the encounter.
You will first receive Honey in Pokémon Brilliant Diamond and Brilliant Pearl after saving the old NPC by defeating two Galactic Grunts in Floaroma Meadow. There are a few honey trees in Florian Meadow, so you can start spreading them right away. In total, there are 21 honey trees scattered around the map.