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Moon Zappa says a "delusional" fan of her famous dad is harassing and threatening her so badly ... she's had to run to court for protection.

Frank Zappa's daughter filed for a restraining order Thursday in L.A. County against a man who's allegedly been stalking and threatening her since 2000. She says way back then the FBI got involved because the man made a death threat against her.

In the docs, obtained by TMZ, Moon says the written death threat said, "I have made plans to murder Moon Zappa. If you want to stop me, contact me now. I know where she is. I know how to get at her. Pumpkins will be barking at that time. I have time on my hands. And soon blood as well."

Moon says she got a restraining order back in 2001 and changed her address -- but her fears were reignited last week when the man showed up on her doorstep on 9/11. She says he handed her a $50 million lawsuit involving a "delusional vendetta" against her.

According to the docs, Moon says the "delusional fanatic" believes she and her father stole lyrics from him way back in the late 1970s. Moon now fears not only for herself, but also for her daughter's safety.