Escolar masquerading as white tuna. Flounder passing for Vietnamese catfish. Pricey baby cod replaced with lesser quality hake instead. Once fish is filleted and skinned, it can be difficult to distinguish, as a Boston Globe investigative report found after testing 183 pieces of fish and finding that 87 were mislabeled. This type of fraud has long vexed the seafood industry, especially for popular species such as red snapper, wild salmon and Atlantic cod, which could be mislabeled as much as 70 percent of the time. But all this fishy business could soon change.

The U.S. Food and Drug Administration, often criticized for less-than-rigorous inspection and enforcement efforts when it comes to seafood fraud, is rolling out new DNA-sequencing equipment in nine of its major laboratories across the country in a push to squelch this type of substitution. Officials say they are targeting cod, grouper, snapper, tuna and other high-value species (which are more likely to be substituted), and have already begun sequencing samples taken from retailers and wholesalers.

The FDA has been looking into such genetic identification—called DNA bar coding—since 2007, when toxic puffer fish from China entered the country labeled as monkfish and sickened several people. At the time the standard way of testing seafood was though protein analysis (through so-called isoelectric focusing). But the technique was not effective if fish samples were processed or cooked.

At the same time, the FDA began working with scientists from the University of Guelph's Consortium for the Barcode of Life (BOL) project, which was compiling a library of genetic data using DNA bar coding as a way to identify all the world's species. Part of that effort included the sequencing of genes of more than 8,200 varieties of fish. Although the BOL project is vast and still growing, it is not designed to be a regulatory database.

So the FDA, in conjunction with the Smithsonian Institution's Laboratories for Analytical Biology and the Division of Fishes, established its own library, ensuring results would hold up in court. "Anyone can put sequences in the BOL," says Jonathan Deeds, FDA research biologist and project head. "Most are good, but there are also a small number of guesses. We needed to have our own database."

The agency set out to validate the method and standardize it in a way that it would be consistent in each of the FDA laboratories. Whereas that process was underway, the cost of DNA-sequencing equipment came down dramatically, from approximately $400,000 per machine to $150,000. According to Deeds, the cost for the FDA to run a DNA barcode test on a fish sample (not including labor and supplies) is only $10. By comparison, tests for seafood contaminants such as polychlorinated biphenyl (PCBs) or polycyclic aromatic hydrocarbons (PAHs) can run as high as $1,000 a sample.

The drop in cost is significant for the successful enforcement of labeling rules, says Gavin Gibbons, National Fisheries Institute (NFI) spokesman. "If we get to a point where there are hundreds or thousands of samples flowing into FDA labs, [testing and enforcement] could have a substantial impact on fraud."

The FDA's library went live on November 1st and is now available to the public and outside laboratories. It contains DNA bar codes from 250 species of frequently consumed fish, each identified by an expert using a specimen held at the Smithsonian as a reference. Another 400 specimens gathered in the Philippines are currently being identified; the agency is also developing a crustacean database covering species like shrimp, lobster and crab. Deeds says he expects the library to double in size in the next few months. (The cost has dropped so much that Deeds says the FDA is also starting to look at mislabeled pet foods and wild game meat using the same technique.)

Analysis requires only a gram-size sample of fish to produce an accurate reading. And with DNA bar coding, the fish can be raw, frozen, steamed or even deep-fried. (Deeds says sampling from canned fish is trickier because temperature and pressure breakdown the DNA, making it more difficult to get results.) Consumers will not be able to send their own samples to the FDA, but if they believe fraud has taken place, they can file a complaint with the agency, which may then conduct its own investigation.

In the meantime, private labs like ACGT, Inc., believe DNA testing of seafood is a business niche worth cultivating and are confident that seafood importers, wholesalers and retailers will embrace it, especially when the testing can come out to mere pennies per sample. "Even if the FDA ramps up its testing, with the amount of fraud going on, it can't monitor the entire industry," says Edward Diehl, director of business development for ACGT. "Is that something people are interested in paying? We'll find out. Increasingly, companies are starting to see that mislabeling affects their bottom line, and consumers are noticing that testing is being done. Pretty soon, they're going to demand it."

Since ACGT launched their seafood testing at the beginning of 2011, Diehl says his firm sees an average of 20 to 25 percent of the seafood samples fraudulently labeled to appear as a higher value fish. Although there is no official figure for how much seafood fraud takes place or costs, NFI spokesman Gavin Gibbons estimates it is in the tens of millions of dollars every year. An Oceana report found that at least 4.5 million kilograms of frozen catfish was sold as grouper or sole in the U.S. in just one year, netting $63 million, to take one example.

DNA bar coding is not foolproof, however. Although it can differentiate between Atlantic cod and Pacific cod, distinguishing a cod caught from George's Bank versus the Gulf of Maine is not easy unless the test is designed to look for a specific genetic marker. The same problem can happen when testing between the closely related northern bluefin and Pacific bluefin tuna, both of which face intense fishing pressure and population declines. And the ability to tell the difference between a fish that has been wild-caught or farm-raised gets complicated quickly, given that they share the same genetics, although there are other methods to distinguish them.

But testing methods are continually improving, and Deeds says portable sequencers for bar coding, which would allow inspectors to verify labeling of the species at the source, is not science fiction. With the necessary funding, Deeds says it could happen in the next few years. In the meantime, consumers should soon feel more confident about the identity of the catch of the day.