IN 2006, beekeepers in Pennsylvania’s apple country noticed the first sign of many bad things to come. Once thriving beehives were suddenly empty, devoid of nearly all worker bees, but with an apparently healthy, if lonely, queen remaining in place. Over a period of just three months, tens of thousands of honeybees were totally gone. Multiply this across millions of beehives in millions of apiaries in the more than 22 states that were soon affected, and suddenly we faced a huge, tragic mystery. Up to 24 percent of American apiaries were experiencing colony collapse disorder (C.C.D.).

Despite the new name for this phenomenon, C.C.D. is not an isolated or unprecedented event. Unexplained mass bee die-offs have occurred throughout recorded history, including some as far back as the years 950, 992 and 1443, when Ireland’s beekeepers noted remarkably high mortality events. Reports from the Cache Valley in Utah in 1903 described thousands of dead hives; around the same time, the Isle of Wight in England faced a near total loss of honeybees.

I became a beekeeper in 2005. When C.C.D. started, I was studying how social animals like honeybees resisted disease. We still don’t really know why C.C.D. was happening, but it looks as if we are turning the corner: Scientists I’ve spoken to in both academia and government have strong reason to believe that C.C.D. is essentially over. This finding is based on data from the past three years — or perhaps, more accurately, the lack thereof. There have been no conclusively documented cases of C.C.D. in the strict sense. Perhaps C.C.D. will one day seem like yet another blip on the millennium-plus timeline of unexplained bee die-offs. Luckily, the dauntless efforts of beekeepers have brought bee populations back each time.

While this is undoubtedly good news, we cannot let it blind us to a hard truth. Bees are still dying; it’s just that we’re finding the dead bodies now, whereas with C.C.D., they were vanishing. Bees are still threatened by at least three major enemies: diseases, chemicals (pesticides, fungicides, herbicides, etc.) and habitat loss.