The Harrogate Autumn Flower Show will use specialist technology to ensure the winning fruit is of the Gigantomo variety.
The giant entries must be from that strain of plant to win the Â£1,000 prize.
It comes after competitors raised concerns unscrupulous growers might sneak in a rogue type of tomato.
Show director Nick Smith said they wanted to be certain the winner "had the right pedigree."
"Giant veg growing is great fun and tremendously popular with our visitors, but it also has a serious side, especially with such a big prize at stake," he added.
The Gigantomo class, developed for its huge red fruits, was launched in January, with the final weigh-in on Friday.
Plant specialist and prize sponsors Van Meuwen said it is the product of almost two decades work by breeders in the UK and United States.
Dutch specialists will test the plants to make sure the entries are what they claim to be and the winner could scoop a further Â£5,000 if the heaviest fruit sets a new world record.
The Guinness record for the heaviest tomato stands at 7lb 12oz (3.5kg).
Gardeners trying to cheat their way to the top tomato prize at a horticultural show will be weeded out with DNA tests.