Captain Gills is a fish from Super Paper Mario. As an infant, he used to be Pook's pet and is kept in a cup until he grew too big for it, then is transferred to a Goldfish Bowl given by Merlon. It turns out Mario needs that fish bowl as a Space Helmet for Chapter 4-1, so Pook was asked for it back. He would only accept to give it back if they gave Captain Gills a new home, for he was growing even too big for his own fish bowl. Mario, Peach, and Bowser had to free him into the underground canal of Flipside's B1st Floor.
After every chapter, Captain Gills got bigger and bigger until, at the end of the game, grew to his largest size and became the master of his own canal. He has grown big and scary, and seems to have survived by turning carnivorous. (Three piles of unidentified bones can be found at the canal's floor as well as many more bones when Mario flips into 3-D.) Although Pook will still ramble about how much he wishes to see Captain Gills (and that he was actually going to see him on his travels out on sea), Tiptron states that Captain Gills, in this form, no longer needs any little children in his life.
He is the only fish in the canal, but somehow, got his own children: Gills Jr., Gills II, Gills III, Gills IV, and Gills V. (Tiptron credits the Stork as to how they came to be.) He has raised all of his children to be carnivores like him.