Greg Mayhew, captain of the 75-foot dragger Unicorn out of Menemsha, is the last Vineyard fisherman still groundfishing on Georges Bank. And this year might be his last on the legendary fishing ground.

“I don’t know if I’m going to even go next year because it might be better just to lease the days out and get half price for them,” he said.

Mr. Mayhew’s story is familiar to small owner-operated fishing outfits throughout New England, who under the new catch shares fisheries management system have found themselves saddled with small catch allocations and burdened by new regulations intended to bring accountability to the capture of fish species in federal waters that have been pushed to the brink of extinction in recent decades.

The catch shares system was enacted this year.

For the National Marine Fisheries Service, which administers the program, it has been a difficult balance between making sure there are still fish to catch and making sure there are still fishermen to catch them.

Under catch shares, each fisherman is allocated a quota of poundage for certain species of fish, replacing the former days-at-sea system that allocated time on the water. Conservationists believed the days-at-sea system contributed to the collapse of groundfish stocks in recent decades. Now fishermen belong to one of 19 sectors in New England, each of which has its own quota of total allowable catch. NOAA, the federal agency that oversees the fisheries, claims that the new system signals the end of overfishing and has already allowed several groundfishing stocks to rebound.

But for small fishermen like Mr. Mayhew, the benefits have been harder to appreciate.

Catch share quotas are administered based on a fishing vessel’s catch history. But that history is based on landings from 1996 to 2006, a period when the factory fleets were about the only ones still trawling on Georges Bank. As a result, Mr. Mayhew said, the most irresponsible fishermen were rewarded while 50-year veterans and small fishermen like himself, who had earned their living fishing for cod in the early 1970s and 1980s before cutting back in recognition of the need to save the stocks, have earned only nominal allocations.

“I feel like the foxes were in the henhouse when they set up this whole catch share allotment system,” Mr. Mayhew said. “They don’t recognize or reward a boat that was conservation-minded and avoided stocks when they were at their low point and went after things like squid or swordfish, so as a result we’ve basically been left out in the cold. Those guys out there now were running around in diapers if they were even born when we were catching cod. If they had only based it on a weighted system with the owner operation and length of time served fishing taken into partial consideration, it would have been a help.”

Instead, Mr. Mayhew said, large, consolidated, politically-connected fishing fleets from central ports like New Bedford and Gloucester have been the biggest winners in the quota allocation sweepstakes.

Aaron Dorrity is the sector manager for the Northeast Coastal Communities Sector that includes the Vineyard. He is based in Penobscot, Me., but the sector — which he developed with the late Vineyard fisherman Tom Osmers in order to give a larger voice to small, community fishing businesses in New England — also includes fishermen from Provincetown and four members from the Island. Greg Mayhew and his son Todd are the only active members. For small fishing businesses like those on the Vineyard that were given nominal fishing allocations, fishermen have the option to buy or lease more quota from those with more so-called catch history, but Mr. Dorrity claims that the system is rigged.

“It’s a free market right now for permits and the only way you can increase your allocation is by buying another permit that has catch history associated with it, and that catch history is expensive,” he said in a telephone interview. “So you’re stuck in a Catch 22: if there weren’t any fish to catch during the qualifying years and then you don’t get an allocation to be able to catch the fish, even as they come back, you won’t have the rights to catch them.”

The key to catch shares is monitoring. In order to end the practice of discarding legal-sized fish in favor of larger, higher price-per-pound fish, known as “high-grading,” and to reduce bycatch — the incidental capture of potentially threatened species — boats are randomly assigned at-sea observers. Without monitoring, the catch shares system doesn’t work.

“If you’re allocating pounds of fish and some people are doing everything they can to break the rules and you don’t have monitoring it’s unfair for the people that are following the rules, so monitors are actually a good thing,” said Mr. Dorrity. “It becomes a burden when that cost is passed on to fishermen and disproportionately to smaller boats.”

With large federal cutbacks looming, many smaller fishermen fear they may have to pick up the more than $700-per-day cost of taking an observer on board. Mr. Dorrity said larger consolidated fleets are better able to bear the monitoring costs associated with catch shares. If monitoring costs go up, more small fishermen will be forced to stay home and sell their shares to make a profit, resulting in further consolidation.

When Mr. Mayhew takes an observer on board Unicorn he strenuously avoids what are known as choke species, a species of fish for which he does not have a high catch history.

“My choke species is pollock and I was allocated nine pounds for the year,” Mr. Mayhew said. “A lot of times a pollock could be a 15 or 20-pounder.”

If an on-board observer witnesses Mr. Mayhew surpass his choke species allotment, he can order Mr. Mayhew to stop fishing.

“When we have an observer aboard, I tell my son I’ll distract him by dropping my trousers and you throw the fish overboard before he sees it so that we don’t have to stop fishing,” he said. “If we do surpass our choke species amount what I would have to do then is hopefully get [Aaron Dorrity] by e-mail and see if he could come up with some quota that they have extra sitting around that I could buy so that I could keep fishing. If not, I could be ordered in by the observer and end my trip.”

Mr. Mayhew said it costs him $1,000 to travel to Georges Bank, a price that may become prohibitively expensive if he has to shoulder the burden of picking up the tab for his at-sea observer as well.

Martha’s Vineyard/Dukes County Fishermen’s Association president Warren Doty summarized the situation.

“We had very, very low quotas offered to us and basically nobody from the Vineyard is fishing anymore,” he said. “The tremendous cutbacks in allocations that came in along with catch shares for cod, haddock and flounder have been so severe that our groundfish boats are tied up.”

“I’m the last of the Mohicans,” Mr. Mayhew said.