What was that giant shadow with the glowing red eyes at the end of the Thriller Bark arc? At the end of the Thriller Bark Chapter 490 in manga and episode 381 in anime. I noticed strange giant shadows with glowing red eyes at the background. What could it be? 

Check this image in manga:



In Anime:
As stated in the comments, it's an entity related to the Florian Triangle.


According to Kokoro, many pirate and commercial ships mysteriously go missing every year and, sometimes, a ship will be found sailing without any people aboard. It has also been said that there are many haunted ships with dead bodies sailing across the sea (though, it is revealed that all this is attributed to Brook).

Though, some of the disappearances that have happened in the Triangle can be attributed to Moriah's scheme. Ships have been disappearing mysteriously in it for a long time before he came on his ship, Thriller Bark, ten years before the series. This mystery is confirmed by an unknown ominous entity larger than Thriller Bark that was barely seen by Captain Lola through the fog. It is so large that it completely dwarfs Thriller Bark, the world's largest pirate ship, in sheer size, possibly making it the world's biggest creature to appear in the series thus far.




It may also be possible that it's the trope &quot;Real After All&quot;:

If an episode revolves around a haunting (or alien visitation) (or lake monster sighting) (or whatever) that turns out to be a hoax, the episode will end with a shot of a real ghost/alien visitor/lake monster/whatever.

However, knowing Oda, that is highly unlikely. I just stated it as it is possible that we may never get to know what those entities were.