Once ordinary Gotham sea life, the Joker Fish were first created when the Joker poisoned Gotham's waters with his venom. The toxin was engineered to not affect humans directly, instead he attempts to patent and market his line of Joker Fish to the public, thus gaining royalties for every fish sold.
However, when he attempts to copyright his creation, a terrified patent officer by the name of G. Carl Francis tells him he can't patent a natural resource. The Joker, outraged, threatens to kill Carl at midnight, and despite the best efforts of the Gotham Police Department he succeeds. Joker then announces that he will kill a second bureaucrat if he doesn't get his way.
Batman deduces that the Joker's next target is bureaucrat Thomas Jackson. Batman disguises himself as Jackson in his home in order to protect the official.
However, Joker sends in Jackson's house cat who he poisoned with his Joker Fish. The cat, knowing who his real owner is, attacks Jackson scratching and poisoning him. Although Batman cannot save Thomas in time, he is able to track down and confront the Joker, thus he never receives the patent.
In the non-canon Damian: Son of Batman, a booby trapped Joker Fish is responsible for the supposed death of Batman.
Joker Fish also appear in the episode of Batman: The Animated Series; The Laughing Fish, based on the Detective Comics issue of the same name.