From the Super Mario Wiki
Dark Megabites are pitch-black, silhouette-like Megabites that can be only found in rooms 39, 69 and 96 of the Flopside Pit of 100 Trials in Super Paper Mario. Like Gigabites, these flying skulls appear instantly when Mario, Luigi, Peach or Bowser enter the room they live in. Dark Megabites are almost invincible, taking only one point of damage no matter how strong the attack is; therefore, since they have 8 HP, eight hits are required to defeat them so it is recommended that the player uses Dottie to continuously jump on it without being seen. Just like regular Megabites and related species, they swoop down into their opponents in order to ram them.
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