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On [[February 21]], [[2001]], he was indicted on 12 tax fraud charges alleging nearly $12 million in unreported income between 1993 and 1998. Twelve additional charges were later added against him. He initially pleaded not guilty and, on [[May 25]], crashed his pickup truck into the [[Frisco 1355]] engine on [[Garden Street]], afterwards claiming to have amnesia. He was sent to a federal medical facility for evaluation and was deemed competent for trial. On [[April 12]], [[2002]], he pleaded guilty to two of the initial counts and was sentenced to 79 months' prison and ordered to repay nearly $5 million in back taxes and fines. His fiancée [[Alice Guy]], who also pleaded guilty to tax evasion charges, was given probation and a $50,000 fine.

Patti was released from prison on [[December 15]], [[2005]] — after only 39 months' detention — because of cooperation and good behaviorbehaviour. He has since returned to managing operations at the seafood company. Before serving his prison sentence Patti attempted to steal the adjoining property to Joe Patti Seafood from his siblings. Captain Joe Patti had helped Franks youngest brother acquire West Florida Fish Company, dba American Seafood, in the early '70s. When Captain Joe passed away in 1992 the property was still titled in his name so it passed on to all of his children. On March 6, 2000, Frank Patti, Sr. illegally deeded himself West Florida Fish Company. On August 11, 2006, his brother, Gerard M. Patti, President of West Florida Fish Company filed an affidavit at the Escambia County Clerk of Courts to reverse the erroneous deed. Seven years after Frank Patti, Sr was released from federal prison he illegally filed a Quit Claim Deed on the property again on December 31, 2012.