The arrest of New Bedford, Mass., seafood kingpin Carlos Rafael leaves a ripple effect in New England’s struggling groundfish fleet

As New England fishermen and federal regulators feuded for years over fishing quotas and the catch share system, one figure seemed to stand apart, like a fighter untouched in a steel cage match.While others fought, Carlos Rafael defended his turf, building the biggest Northeast fleet, deriding all challengers — including other fishermen, who raised concerns about his massed groundfish permits.

“They are like mosquitoes on the balls of an elephant,” he famously declared in a rollicking 2013 profile by Vice Media. “The maggots screaming on the sidelines, they’re done.”

That groundfish fleet — at that point down to 15 vessels, operating on 60 permits, according to Rafael — already represented a big part of New England’s fishing power. Now with Rafael, 64, and Carlos Seafood bookkeeper Debra Messier, 60, facing federal charges of conspiracy and falsifying landing reports, it’s anyone’s guess how much damage it did to groundfish stocks — and to the government’s already troubled stock assessments.

In a simple sting operation, federal undercover agents posing as Russian mobsters interested in buying Rafael’s business got him to explain how he was able to sell fish species beyond what was permitted by quotas, by falsifying invoices and other records, according to a court affidavit by Internal Revenue Service agent Ronald Mullett. “Very easy, we own the boats,” Rafael allegedly told the agents.

The affidavit portrays Rafael talking of a scheme practiced for 30 years, decades when he was earlier convicted of tax evasion and false statements on landing reports. Even without public information about the true magnitude of Rafael’s take, the industry is buzzing about what it may ultimately mean for management decisions. Stock estimates for cod and other species have proven so out of whack that a host of theories blame climate change, warmer waters in the Gulf of Maine, sampling errors, or all in combination.

Poaching by Rafael’s fleet is for now one more uncertainty, and NOAA officials say little about where it will lead them.

“There’s no information right now, and I can’t comment on a specific case,” said John Bullard, the Northeast regional administrator for NMFS. “If there is information, it will take years in stock assessments going forward.”

“There’s a lot of questions about permits and other things, but it’s all way premature,” Bullard added.“Unfortunately it’s given the government a... 

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