NEW BEDFORD, Mass. — Carlos Rafael, whose initials are emblazoned on boats all over this port city, boasted that his fishing empire was worth even more than official records showed. His trick? When he caught fish that are subject to strict catch limits, like gray sole or cod, he would report that his nets were filled with something far more plentiful, like haddock.

“We call them something else, it’s simple,” Mr. Rafael told visitors who seemed interested in buying his business. “We’ve been doing it for over 30 years.” He showed off a special ledger labeled “cash.” And he described an under-the-table deal he had going with a New York fish buyer, saying at one point, “You’ll never find a better laundromat.”

But Mr. Rafael’s visitors turned out to be Internal Revenue Service agents, and the conversations, caught on tape and described in court documents, began the unraveling of Mr. Rafael, whose reign over a segment of this region’s fishing industry gave him his larger-than-life nickname, “the Codfather.”

As Mr. Rafael sits in prison, having pleaded guilty to lying about his catches and smuggling cash out of the country, nearly two dozen of his boats have been barred from fishing for species like cod and haddock, grinding part of the centuries-old maritime economy in the nation’s most lucrative fishing port to a halt.