The approval by the U.S. Department of Agriculture this month for new soy and corn seeds by Dow Chemical is setting off another battle over genetically modified organisms (GMOs).
At issue is whether the extended use of GMOs is creating a new type of "superweed."
These weeds are developing resistance to herbicides, because the GMO seeds can tolerate greater use of certain herbicides and pesticides.
As more herbicides are sprayed, that's created stronger, herbicide resistant weeds on farmland, reportedly costing farmers a billion dollars in lost crops.
"It is a crisis situation," said Neil Harker, a weed ecologist at Agriculture and Agri-Food Canada. "We're losing the effectiveness of herbicide tools against weeds going forward."
"I'm in favor of GMOs, but they should be used judiciously," he said.
Others say the weed infestation is one more reason to avoid GMOs altogether.
"We don't need pesticide-resistant GMOs to control weeds. There are natural ways to fight them," said Bill Freese, a science policy expert at the Center for Food Safety.
"The GMO industry likes to put a warm fuzzy glow on GMOs but we don't see much use for them at all," he argued.
However, farmers like Bill Horan, who has 4,000 acres in northwest Iowa, believe GMO seeds are irreplaceable. "We've used GMO corn seeds for decades and they're a great product," said the 66-year-old Horan. "It's always a battle with weeds but with the new seeds, the pesticides work better," he said.
The newest genetically modified corn and soybeans were developed by Dow AgroSciences, a division of Dow Chemical. They are to be sold under the brand Enlist Weed Control System.
The seeds can tolerate glyphosate, the world's most widely used herbicide, as well as the lesser used herbicide called 2,4-D.
While approved by the USDA on Sept. 17, the seeds still need the go-ahead from the Environmental Protection Agency for their herbicide-resistant formula. However, that approval is expected, according to experts, with the seeds going to market in 2015.
The infestation of superweeds has more than doubled since 2009, according to Dow Chemical, which also states that an estimated 70 million acres of U.S. farmland are infested with herbicide-tolerant weeds that cost roughly $1 billion in damages to crops so far.
In an email response to CNBC.com, a Dow spokesperson wrote: "We agree with our critics that with unvarying use of the same model of weed control action ... weeds will adapt. We differ from critics however, in that we believe the best way to promote responsible use of weed control technology is to provide growers with the broadest practicable range of weed control options."
Monsanto also makes the herbicide Roundup, whose chief ingredient is glyphosate.
Read MoreCalifornia's crop harvest much smaller than usual
"(Weed) resistance to herbicides existed prior to the introduction of genetically engineered seeds," wrote a Monsanto spokesperson in an email to CNBC.
"Monsanto has been working for many years with scientists and academics to educate growers on the need for multiple modes of action," the email said.
Because the fight against weeds is hardly new, that's a reason to avoid putting all the blame on GMOs for the current infestation, said Justin Gardner, a professor of agribusiness at Middle Tennessee State University.
"What's going on is natural selection," Gardner said. "Weeds were resistant before GMOs. The best way around this is to use different weed killers instead of the same one all the time."
But the increased resistance by weeds to herbicides only highlights why GMOs are at fault, said Itzick Vatnick, a professor of biology, biochemistry and environmental science at Widener University.
"With the introduction of GMOs engineered to resist glyphosate in the mid-1990s, genetic resistance of many weeds to it rose dramatically," he said.
"The problem is so severe that the agrochemcial companies are now poised to introduce herbicides that are more toxic," Vatnick argued.
The superweed infestation is unlikely to end the debate over GMOs. If anything, it just deepens the divide, say analysts.
The companies that make GMOs vouch for their safety and continued use. Bill Horan sees them as life-changing.
"We don't have weeds anymore, so we can take time to do the little things like going to our kids' swim team lessons," said Horan, who's harvesting his 40th corn crop this year.
"We couldn't do that when I was growing up when we didn't have the GMOs," he said.
But the critics point to what they say is a continuing list of harmful effects.
The Center for Food Safety's Freese said increased herbicide use—because GMOs are more herbicide tolerant—are decimating the monarch butterfly population in the U.S.
Freese said it's decreased by 90 percent due to herbicides killing off the milkweed that is a natural habitat for the butterflies.
John Kempf, a farmer and CEO of Advancing Eco Agriculture, a soil nutrition consulting firm, said GMOs fail to match their claims.
"They don't increase crop yields and they increase the resistance of weeds to herbicides," he said. "We should use the science of nutrition for the soil instead of the science of GMOs."