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The Elite Marks, whilst not exactly being hidden, could qualify as hidden bosses as some of them require conditions being met to fight them. Yiazmat is the most famous of these whom you fight in the Ridorana Cataract after defeating a certain mark.

Alternatively there are also the espers whom you have to fight, I believe only a couple of these are obtained during the main story, others like Cuchulainn, Adrammalech, Ultima and Zodiark require you to go out of your way and,in the case of Zodiark, have an extremely advanced party.

There is also the optional bosses Omega Mk.XII, Hell Wyrm, and Elder Wyrm, who isn't in any way actually secret but, from what I've heard, is infact optional if you're willing to fight through hordes of high-level Hellhounds and other such creatures.

Elder Wyrm isn't a secret boss, you fight him in the main story line. Omega Mk XII is a superboss, and is insanly hard to kill conventionally

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