Bees are overworld enemies that appear when Link disturbs certain trees. Bees usually attack in groups, and can be difficult to deal with.
A Link to the Past
Bees are enemies that appear in The Legend of Zelda: A Link to the Past. They sometimes appear when Link dashes into trees with the Pegasus Boots. Some times a single bee will appear, other times a group of bees will appear. Bees can be caught and stored in a bottle using the Bug Catching Net.
A rare version of the bee also appears in A Link to the Past, gold in color. This bee is more powerful as an ally in combat than the regular bee. You can also sell the Golden Bee in Kakariko Village for 100 rupees.
Four Swords Adventures
Some trees on Cannon Island have beehives on them. When Link rolls into these trees, the bees will emerge and attack relentlessly. A spin attack is the best way to defeat them. Bees also appear on Dee Ess Island in random spots on the ground. You'll only know they're there after digging them up.
When Link rolls into or hits a tree with a beehive, the bees will come out and attack. They'll go away if you jump into water or enter a new area. Sometimes, the beehive will drop Bee Larvae. Besides opening chests, this is the only way to obtain Bee Larvae.