“We were saying, catch shares are going to lead to consolidation, catch shares are going to lead to integration, catch shares are going to lead to corruption,” said Scott Lang, a former mayor of New Bedford.

Mr. Rafael came to control most of the permits for groundfish in his sector, but by 2015, he was pondering selling his business. His asking price: $175 million.

So when the I.R.S. agents — who posed as Russian mobsters interested in buying Mr. Rafael’s business — came along, Mr. Rafael was quick to talk to them.

Explaining why his business was worth even more than it might appear to on paper, Mr. Rafael laid out all that he had done to misreport what fish he was catching. At points, he seemed to worry that he might be getting set up. “You could be the I.R.S. in here,” Mr. Rafael said in one recorded conversation, though he swiftly dismissed the idea, noting that he didn’t think the I.R.S. employed Russians. “That would be some bad luck!”

Last year, in a case that married international financial crime with flaky fish fillets, he pleaded guilty to conspiracy, tax evasion, bulk cash smuggling, false labeling and falsifying records. In September, he was sentenced to about four years in prison as he stood before a courtroom packed with fishermen who had worked for him.


Carlos Rafael in New Bedford in 2014.

John Sladewski/Standard Times, via Associated Press

“I did it because I wanted to make sure my people kept getting a paycheck,” Mr. Rafael wrote in a statement read by his lawyer. “The waterfront is a hard world we work in.”

The judge, William Young, of the Massachusetts U.S. District Court, seemed unmoved. “This was not stupid,” the judge said, “this was corrupt.”

Mr. Rafael’s lawyer, William Kettlewell, did not respond to messages seeking comment.

Mr. Rafael’s punishment was cheered by environmentalists, regulators, and fishermen up and down the coast who saw him as having muscled out smaller boats and having marred the whole region. The case also raised questions about the effectiveness of a regulatory system that allowed one man to become so dominant and to skirt the rules for so long.

“He’s the biggest player in the most high-profile fishery in New England,” said Peter Baker, with the Pew Charitable Trust’s ocean conservation effort. “They should have been able to detect what he was doing long before they did.”

John Bullard, who was NOAA’s northeast regional administrator until the end of January, said the regulatory system had worked well elsewhere. He said he had banned ground fishing in Mr. Rafael’s sector through at least the beginning of the next fishing season in May because the industry there had failed to accurately report its catches and stay within fishing limits. “They have a very basic job to do, to count fish, and they didn’t do it,” said Mr. Bullard, who is also a former mayor of New Bedford.

The future of Mr. Rafael’s empire is a matter of intense debate. Federal authorities have seized some of his boats and fishing permits, and they are seeking to revoke more permits in a civil action that also asserts misreporting in Mr. Rafael’s scallop fleet.

Fishermen in other ports hope Mr. Rafael’s permits will be transferred to their areas, while fishermen in New Bedford are fighting to keep them local. Some boat captains worry that they may face scrutiny, even though they say they had no part in Mr. Rafael’s crimes.

(Mr. Rafael told the undercover agents that the captains knew of his schemes; Mr. Lelling, the prosecutor, said a decision was made to go after Mr. Rafael, and not the fishermen working for him.)

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