The number of bee colonies that died in the year since April 2014 reached levels only ever seen once before, reported the Bee Informed Partnership.
Of the total number of colonies managed over the past 12 months, U.S. beekeepers said 42.1 percent were lost. It was the second-highest annual loss recorded.
Annual beehive losses varied across the nation, with the highest in Oklahoma at 63.4 percent and the lowest in Hawaii, with 14 percent.
During this past winter season, the Bee Informed Partnership gathered data from 6,128 beekeepers in the United States who managed 398,247 colonies as of October 2014. That represents about 14.5 percent of the estimated 2.74 million managed honey bee colonies in the country.
Winter die-offs were reported to be 18.7 percent, which is quite a bit lower than the nine-year average total loss of 28.7 percent, the partnership noted. But bees don't just die in the winter; they perish in the summer too.
From April to October 2014, the summer colony mortality eclipsed winter numbers, with beekeepers reporting 27.4 percent of colonies gone, compared with summer losses of 19.8 percent in 2013.
"Importantly, commercial beekeepers appear to consistently lose greater numbers of colonies over the summer months than over the winter months, whereas the opposite seems true for smaller-scale beekeepers," the Bee Informed Partnership said in its press release.
The Bee Informed Partnership gets most of its funding from the National Institute of Food and Agriculture, USDA.
While the cause of ongoing bee colony failure hasn't been fully pinned down, it's widely accepted that pesticides - specifically neonicotinoids - are one of the biggest reasons that bees are dying, threatening the national food supply. Other causes are bad nutrition and pests.
"These dire honey bee numbers add to the consistent pattern of unsustainable bee losses in recent years that threatens our food system. The science is clear - we must take action now to protect these essential pollinators from bee-toxic pesticides." said Tiffany Finck-Haynes, food futures campaigner with Friends of the Earth, in a press release.
The U.S. government is starting to do just that. On April 2, the Environmental Protection Agency put a freeze on new or further uses of neonics while it evaluates the risks for all pollinators.
And last October, federal facilities and federal lands were instructed to buy seeds and plants from nurseries that don't treat them with base-level insecticides like neonics.
Perhaps most importantly, home improvement stores like Home Depot and Lowe's are starting to take measures to remove neonics from their stores.
Study co-author Keith Delaplane at the University of Georgia told the AP that the honeybees, which are very visible, are basically canaries in a coalmine, a sign that there are "bad things happening with our ago-ecosystems."
"The solution to the bee crisis is to shift to sustainable agriculture systems that are not dependent on monoculture crops saturated in pesticides. It's time to reimagine the way we farm in the United States and incentivize organic agriculture practices that are better for bees and for all of us," Finck-Haynes said.