The long and brutal winter was especially unkind to the iconic Chesapeake Bay blue crab.

How cold was it? More than a quarter of the crustaceans perished in the icy water, one of the worst winter die-offs recorded in the bay.

And in an alarming finding, female crabs were hit hardest. Only 69 million were counted in the annual winter crab survey, released Thursday by Virginia and Maryland. The number of females, a 12-year low, is not enough to sustain the overall population, officials said.

The total number of crabs projected by the latest survey — 297 million — continued a downward trend that started last year, following the remarkably high estimate of 765 million in 2012.

“This is disappointing news,” Virginia’s marine resources commissioner, John M.R. Bull, said in a statement.

The two lower-bay states have two options: conserve females by reducing the number that can be taken in the March-to-November open crab fishery, or conserve this year’s bumper crop of juveniles “to increase their chances of reproducing in even larger numbers next year,” Bull said.

The National Oceanic and Atmospheric Administration said 160 million to 215 million females are needed to raise the crab population to its estimated 1991 strength of 828 million.

Watermen who catch and sell crabs for a living will have to cut their harvests, which will lower the number of Maryland blue crabs available for grocers and restaurants.

The winter dredge survey performed annually by the Virginia Institute of Marine Sciences and the Maryland Department of Natural Resources is the primary means of determining how many crabs are in Virginia and Maryland waters.

Scientists take samples at 1,500 sites in the bay watershed starting in December and ending in March. During that time, female crabs bury themselves in mud to wait out winter. Their immobility allows “scientists to develop, with good precision, estimates of the number of crabs present in the Bay,” according to a statement released by the agencies.

The Chesapeake Bay’s blue crab population has swung between highs and lows — with mostly lows — since the survey started. Juvenile crabs were one of the few bright spots in this year’s survey, up 78 percent from a record low last year.

But Maryland and Virginia officials were not upbeat about the situation, noting that juveniles remain at pre-2008 levels. That year, Maryland’s DNR, the Virginia Marine Resources Commission and the bi-state Potomac River Fisheries Commission launched a baywide stock-rebuilding program.

Representatives of the three agencies, which oversee the crab fishery, plan to meet in the coming weeks to determine a way forward.

One thing is nearly certain: Virginia’s winter dredge fishery, in which watermen harvest mostly females by scouring river bottoms, will remain closed for the sixth year. But Virginia watermen are still licensed to set 300,000 crab pots each year.

In an attempt to better monitor the crab fishery, Maryland officials have encouraged watermen to use digital phones and tablet computers, instead of pen and paper, to more accurately log the numbers of males, females and juveniles caught and released.

Crab populations fluctuate naturally, but the size of the harvest appears to have an effect. When the crab population reached 828 million in 1991, watermen harvested 90 million pounds, far too much, biologists argued. The next year, the population plunged to 367 million.

Several years later, the pattern was repeated. In 1997, watermen harvested 77 million pounds from a stock that had rebounded to 680 million. The next year, the population fell to 353 million.

Two years ago, the population hit 765 million, a 21-year high, and watermen took 56 million pounds. Last year’s harvest was only 37 million pounds, the lowest since 1990, according to the survey. But the frigid water took a huge toll.

“Even though our 2008 conservation measures were designed to allow for naturally occurring fluctuations in crabs, these results are not what we had hoped to see,” said Tom O’Connell, Maryland’s fisheries director.