Mr. Krabs was formerly married to a whale, Pearl’s mother. He mentioned that Pearl is his biological daughter. However, she takes after her mother. This was only revealed in the official trivia book, written by former episode writer David Fain.  According to show creator Stephen Hillenburg, he only made Pearl a whale rather than a crab because he wanted to have different animals for the main cast. This is the more plausible reason why Krabs' daughter is a whale.