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Bees appear in Yoshi's Story, where they fly around their Beehive, not letting Yoshi pass. Yoshi has to walk slowly to prevent the Bees from bothering him. Other larger Bees also appear in Yoshi's Story, as enemies that sting Yoshi if he gets too close.
Super Mario series
Super Mario Sunshine
In Super Mario Sunshine, various Beehives can be found in Bianco Hills, Gelato Beach, and Pianta Village. If Mario gets too close to a Beehive or knocks one down, the Bees swarm him, causing damage if he gets stung. Yoshi can eat these Bees for one Coin each. The last Bee to be eaten always gives a Blue Coin or 1-Up Mushroom.
Mario & Luigi series
Mario & Luigi: Bowser's Inside Story
Mario & Luigi: Dream Team
Bees reappear with Beehoss enemies in Mario & Luigi: Dream Team. They now have spikes on their head.
Super Smash Bros. for Nintendo 3DS / Wii U
In Super Smash Bros. for Nintendo 3DS / Wii U, a Beehive item appears which, when thrown at an opponent, releases a swarm of Bees that attacks them. However, if a player attacks a Beehive directly, the Bees go after them instead.
Mario Party 10