For many sea anglers it could be the end of the line. The European Union wants to impose quotas on recreational fishermen limiting the number of fish they may catch.

The move is designed to protect endangered species such as cod, ling, pollack and shark. The EU sets tight quotas on commercial fishermen for these species – but anglers have no such restrictions.

In the past decade, however, sea angling has surged in popularity. A survey by the Maritime and Coastguard Agency suggests that about 1.4m people in the UK take part each year.

Many of them take huge catches and these are often sold commercially to fishmongers and dealers. By contrast, the number of commercial fishermen in Britain has fallen from 18,600 in 1997 to 12,700.

The EU believes the recreational sector is now so big that anglers can have a significant impact on the populations of endangered species – so it must be controlled.

Joe Borg, European commissioner for maritime affairs and fisheries, said: “Control and enforcement of catch limits should be the cornerstone of the common fisheries policy. The future of sustainable fisheries requires us to replace a system which is inefficient, with one which can really produce results.” Under Borg’s plan, each EU state would be given a quota for each protected species. Governments would then divide this quota between commercial fishermen and anglers. Anglers would be banned from marketing their catches.

He wants to make recreational boat skippers apply for a licence for their boat and stop fishing when their quota has been reached. They would be subject to modern fisheries inspection technology, such as the satellite-based vessel monitoring system, electronic log-book and electronic reporting of catch data.

The move comes as scientists increasingly support the eating of fresh fish as part of a healthy diet. The trend has been popularised by celebrity chefs – Rick Stein has published several books of fish recipes – but some question whether it is ethical to eat some fish species.

Last year Hugh Fearnley-Whittingstall, a sea angler since childhood, published The River Cottage Fish Book. However, this autumn he wrote: “Until recently, the biggest question to furrow the brow of would-be fish eaters was, ‘How do I cook this?’ In this age of dwindling stocks, that has been replaced by, ‘Is it okay to eat this at all?’ ” The notion that hobby anglers pose a big threat to marine fish has won increasing scientific support. The journal Science published a study by Felicia Coleman of Florida State University showing that anglers are the largest human threat for many species off America. Other research suggests the same is true around Europe.

Anglers disagree, with many seeing the measures as an attempt by the commercial sector to impose “equality of misery” on recreational fishermen.

They also point out that British anglers spend about £1 billion a year on equipment, boat hire and accommodation.

Many ports such as Weymouth, Littlehampton, Seahouses in Northumberland and Arbroath in eastern Scotland have flourishing angling fleets that earn tens of millions of pounds a year.

The Department for Environment, Food and Rural Affairs said it would hold discussions with angling organisations next month.

Chris Caines, 57, who runs fishing trips from Weymouth to the Channel Islands on Tiger Lily, his 36ft catamaran, fears bureaucracy would kill the business.

“While trawlers using nets are having to dump their catch in the sea because they have gone over quotas, it seems ridiculous to ask people to log one or two they catch,” he said.

However, Callum Roberts, professor of marine conservation at York University and author of The Unnatural History of the Sea, welcomed the move. “People today find it hard to understand how much damage we have done to the seas around Britain. We have destroyed about 95% of the species that used to live there,” he said.

“Things like herring used to be unbelievably abundant. The shoals would cover thousands of square miles surrounded by armadas of predators that fed off them, ranging from sea birds to whales. Now they are all gone.”

Additional reporting: Sofia Zabolotskih

Times recommends

• Energy-saving ideas from switched-on professor
• Rooks are as clever with tools as chimpanzees
• Burping of the lambs blows roast off menu