Older laboratory techniques to identify fish meat looked at the mix of proteins in flesh samples, but were unreliable, expensive and cumbersome. Investigators often relied instead on laborious legwork, tracking inconsistent fish names on paperwork as seafood moved across international borders. Eighty-four percent of seafood consumed in the United States is now imported, often passing through a multistep global supply chain.

With the new genetic techniques, the gene sequence found in a fish sample is compared with an electronic reference library like that maintained by the International Barcode of Life Project, which now covers 8,000 varieties of fish compiled by biologists over the last five years. The testing is now relatively cheap: commercial labs charge about $2,000 for analyzing 100 fish samples, for an average of $20 apiece, but the cost is under $1 per sample for labs that own the equipment.

Image A mako shark fillet, above, is often passed off as swordfish, top. Credit... NOAA

Douglas Karas, a spokesman for the F.D.A., said in an e-mail that the agency had been working with scientists to “validate” DNA testing for several years. It recently purchased gene sequencing equipment for five F.D.A. field laboratories and hoped to use it “on a routine basis” by the end of this year.

This new type of scrutiny could allow hundreds of thousands of samples to be tested each year, rather than the hundreds that are now rigorously analyzed, said Dr. Paul Hebert, scientific director of the Barcode of Life project, based in Guelph, Ontario. In March, the F.D.A. issued an alert to inspectors about mislabeled fish. It had already used bar coding as irrefutable evidence to prosecute sellers or issue warnings involving seafood “misbranding,” Mr. Karas said, much as prosecutors use DNA evidence in sex crime cases.

But it will take time to clamp down on a lucrative and, apparently, widespread practice. Dale Sims, chief fishmonger for Cleanfish, a San Francisco-based supplier of high-end sustainable seafood, said he’d seen thresher shark labeled as shark, swordfish and mahi-mahi all in the same market, as well as many other obvious substitutions.

“It infuriates me but it’s hard to correct,” he said. “I’m embarrassed to say that there’s been a lot of fragmentation in this industry. So if someone is unscrupulous, it’s been easy to get away with it.”