On a chilly morning last winter, Tom Theobald refined beeswax in his “honey house,” a small brick building on a hillside in Niwot. The lumbering man stooped over an aromatic pot of golden-tinged wax, carefully filtering it of impurities and pouring it into molds. Later he’ll remelt the wax to make candles.

A beekeeper for more than 30 years, Theobald makes a part-time living from honey and candles produced from his 80 colonies of bees. But all is not well in the world of beekeeping, and Theobald says there may not be many winters left in the honey house. Like beekeepers all over the country, Theobald opened his hives last spring to find that many of his colonies had simply vanished.

“We send a colony into the winter full of bees and heavy with honey, and they just disappear,” says Theobald. “We haven’t seen anything like it before.” Bruce Boynton, CEO of the National Honey Board, says that in Colorado some commercial beekeepers lost as many as 40 percent to 60 percent of their hives last winter. Nationwide, beekeepers reported losses of 30 percent to 90 percent in 2006. Stumped, researchers named the phenomena Colony Collapse Disorder, or CCD, and the few bee research laboratories in the U.S. put their scientists on the case.

Beekeeping is critical for agriculture, explains Boynton. In Colorado, many farmers rely on commercial beekeeping operations to pollinate local crops, from onions to fruit trees. Says Boynton, “If there are fewer bees, pollination fees are going to go up, increasing food prices to consumers.”

A study published in the journal Science last fall identified a possible culprit: a virus known as Israel Acute Paralysis Virus (IAPV), which may have been imported from Australia. However, a second genetic analysis published in the American Bee Journal found that the virus had been present before the widespread import of Australian bees—and long before the identification of CCD.

Many researchers suspect that the disorder results from a complex interplay of factors, rather than a single disease or parasite. Commercial beekeepers commonly truck their hives thousands of miles to pollinate crops, a practice that can put stress on an already weakened population. Some suspect a new class of pesticide called neonicotinoids, a class of nerve toxins that are highly toxic to insects but relatively harmless to other animals. Chronic exposure to the pesticide might interfere with the bees’ memory, leaving them unable to find their way back to the hive. Others speculate that a common pest, the Varroa mite, might weaken the bees’ immune systems and make them more susceptible to otherwise mild infections.

Whatever the underlying cause, beekeepers, farmers, and honey industry officials are hoping the crisis will bring more research money and public attention to the decline of honeybees and other pollinating insects. Even before the epidemic in 2006, U.S. bee populations were steadily deteriorating. May Berenbaum, head of entomology at the University of Illinois at Urbana-Champaign, said in a statement to Congress last year that if honeybee populations continued to decline at the same rate as they did from 1989 to 1996, beekeeping would be nonexistent by 2035. Says Boynton, “The beekeeping industry has not been given the support it needs to maintain itself. If the cattle and sheep industries had sustained the kind of losses that beekeepers have sustained, they would have gotten a lot more attention.”

Some local beekeepers worry that the current attention to honeybees may be too little, too late. Tom Theobald returned to his bee fields late this winter to find that he’d already lost half of his hives. “We’ve been leading up to this crisis for years,” says Theobald. “It’s not going to take too many more winters like this and I’m just going to be gone.”