The blue crab, the Chesapeake Bay’s most valuable catch and a closely watched proxy for the health of its underwater ecosystem, is less abundant now than at any other time since scientists began regularly tracking the species in 1990.

The new winter dredge survey conducted by the Maryland Department of Natural Resources and Virginia Institute of Marine Science and released May 19 found an estimated 227 million crabs in the bay. The previous low was 270 million crabs in 2004.

Year-to-year population fluctuations, even dramatic ones, are common for the species. Fishery managers say the plunge wouldn’t be so concerning except that it has been accompanied by a three-year streak of below-average reproduction.

And they aren’t sure what’s behind the decline.

“It’s shocking in that we’ve had enough females over the last couple years to produce a good year class, and it hasn’t happened,” said Genine McClair, blue crab program manager for the Maryland DNR. “The question everyone has...