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From Code Wiki
Dark Monsters are simply tougher versions of regular monsters that have a darker coloration then the normal variety. So far, the only dark versions of monsters have been of the Roachster and the Hornet in the Code Lyoko DS video game, but it is possible that William's Black Manta may fall into this category as well. Dark Monsters have the same weaponry as their normal counterparts. However, their weapons do more damage and they have more life points. These Dark Monsters have not appeared in the show so far. Some Dark Monsters also appeared in Code Lyoko: Quest for Infinity