Sometime early next month, Carlos Rafael is expected to report to a federal prison to begin serving a 46-month sentence for criminal conspiracy and tax evasion.

Rafael, the 65-year-old New Bedford-based fishing magnate, admitted to a judge earlier this year that he had lied to federal fishing regulators about the nature and size of his groundfish landings and bulk smuggling.

At sentencing last week, U.S. District Judge William G. Young rejected the argument from the man who liked to call himself “The Codfather” that the fraud was necessary to protect the jobs of his workers.

“This was stupid,” Young told Rafael. “This was a corrupt course of action from start to finish. It’s a course of action of extensive corruption designed to benefit you, to line your pockets. That’s what it is and that’s why the court has sentenced you as it has.”

Good for Young for handing down a stiff sentence (Rafael was seeking probation). The Codfather’s story, however, does not end here. His arrest and prosecution laid bare a broken regulatory and monitoring system.

It’s inexplicable how investigators came to the Rafael grift so late. Rafael’s boats landed hundreds of thousands of pounds of cod, a chronically overfished species, skirting catch limits by labeling the catch as species like haddock and flounder, which are less-valuable and more plentiful. The scheme let The Codfather circumvent catch limits on cod while paying lower taxes on the value of his catch.

The fraud was so widespread that there is legitimate concern that the false filings skewed fishery scientists’ fish count by millions. Such counts — reported by fishermen — play a large role in management decisions. Regulators need to trust that fishermen’s reports are accurate, and fishermen need to know the federal government is making decisions based on solid data. Rafael’s scheme damaged that trust.

The federal case against Rafael covered only four years; the Codfather has been working the waterfront in New Bedford for more than three decades, calling himself a “pirate” and daring regulators to catch him. It took them too long to do so.

Now that Rafael is headed for prison, regulators still have no idea what to do with the fishing permits and property he amassed over the years. The fishing magnate proposed forfeiting the 13 groundfish permits he used in his scam.

Rafael’s wider empire, however, consists of a fleet of more than 30 boats, 40 permits and other assets totaled at more than $100 million.

Some in the industry want to see the forfeited permits handed out across New England or Massachusetts, rather than returned to New Bedford interests. Those in that city, however, have a fishing tradition that mirrors Gloucester’s, and the loss of those permits could be the death knell for groundfishing there. John Bullard, the outgoing regional NOAA administrator, has a difficult decision to make. Gov. Charlie Baker has floated the not-too-farfetched idea of using Rafael’s forfeitures to pay for onboard monitoring of fishing catch — long a sore point among fishermen who oppose being forced to pay for it.

Bullard’s decision would have been easier — or avoided altogether — if the regulatory system for groundfish was properly designed in the first place. The catch-share system designed for the New England fishery allowed — some would say abetted — Rafael’s efforts to amass his empire. He owned the boats landing the fish as well as the dockside businesses registering the catch, making it easy to hide his scheme from regulators. As large operations like his have grown more powerful, smaller operations — the single, family-owned boats that were once the backbone of the industry — increasingly are left to battle for scraps.

That has to change. Other fisheries — the West Coast groundfishery and Maine’s lobster industry — take steps to make sure no single interest controls the seas. The same should happen here.

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