New Bedford fishing mogul Carlos Rafael pleaded not guilty Thursday in U.S. District Court in Worcester to conspiracy, lying to NOAA Fisheries about the exact species of fish he landed through a four-year span, and illegally smuggling cash out of the country.

Rafael, know widely as “The Codfather,” remains free on the $1 million bond set after his February arrest for conspiracy and submitting falsified records. The arrests of Rafael and his bookkeeper Debra Messier capped an undercover sting operation by federal authorities, some of whom posed as Russian mobsters looking to buy his business.

The 64-year-old Rafael, who appeared before Magistrate Judge David H. Hennessy, controls one of the largest commercial fishing fleets in the United States and has been a powerful force in Northeast commercial fishing circles through his ownership of 32 fishing vessels and a block of 44 federal fishing permits with a value estimated in the tens of millions of dollars.

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