The whale, which was roughly 12 to 15 feet long, was discovered Thursday morning below Atlantic City's Central Pier.
Police tell The Press of Atlantic City the purple markings are not gang-related and appear to be Greek letters.
The letters appeared to be Tau Epsilon Phi, a fraternity that has chapters at several area schools, followed by what looked like "94."
Spokesman Jesse Cohen says while it has not been confirmed that Tau Epsilon Phi members were involved, the fraternity considers it a "reprehensible act" contrary to its teachings and is cooperating with authorities.
A state pathologist will try to determine the cause of death.