He belonged to an unnamed alien species with skull-like faces, fangs, and multiple eyes. Apparently he stole Treasure Planet from a highly-developed species of an unknown name. After many years of looting merchant ships, Flint buried a vast enormous treasure in the center chamber of treasure planet (which is in fact a giant alien mechanism). He entrusted the map to Treasure Planet to his first mate Billy Bones and stole the memory chip of his robot navigator, B.E.N.. Flint also set the whole planet to explode if someone should find his treasure. Shortly after setting up this booby trap, he stayed inside the center of Treasure Planet with his treasure and soon died guarding it.
In the original Treasure Island novel, Captain Flint's name is Captain J. Flint. But it is unknown, what the J. stands for. And in contrast to the one in the movie, the novel version of Flint actually wanted someone to find his treasure, having used a corpse to point the way to it.