Just like in the Mario Forum, who was the toughest boss in a Legend of Zelda game, and which game were they from? It could be a dungeon boss, a mid-level boss... or the final boss. And it can be from any of the games.
Since several of the bosses have apeared in multiple games (at varied dificulties), try to make sure you mention which game the boss is from.
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I have to say the 3rd boss on links awakening i think (or was it a link to the past?)
where you walk into the room and u don't see the boss and and enemys are falling down and you first have to find him then split him in 2 then i forgot the rest.
that took me a while to work out where he was ^.^
I would have to say Vaati from the Minish Cap. He has many forms that you must go through, some pretty nasty attacks and it took a while for me to figure out how to attack him successfully
If I remember correctly my hardest is actuly the 8th boss(I think) from orical of ages(can't spell it)
he changes i think and you have to keep finding out how to take out the new form!
Puppet Gannon from Wind Waker he was hard in his snake form because it is hard to aim at the thing at his tail while dodging his attacks after you beat him its smooth sailing deafeating gannon