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Early rock paintings in Spain and Africa depict people gathering honey from trees or rock crevices while bees flew around them. Ancient Egyptian relics show the beekeeper taking honey from a hive while a helper drives the bees away with smoke. There is evidence that the Mayans kept a stingless, honey-storing bee. Relics from Belize and Mexico, including stone disks thought to have been the end stoppers on wooden log-shaped hives, represent the oldest artifacts related to beekeeping in the New World.

Early honey gatherers probably accidentally discovered that smoke calms bees when they used fire to drive off other animals. Beekeeping may have originally developed following the observation that swarms of bees will settle in any container with a dark, protected interior space. Pottery and natural containers, such as holes in trees or logs, provide shelter and protection for hive establishment. In some forested areas of Europe, hive clusters made from logs can still be found. Horizontal pottery hives are used along the Mediterranean, and straw hives, known as "skeps," are still used in Belgium and France.

The honeybee, which is not native to North America, was shipped to the colonies from England in the first half of the 17th century. For many years, straw skeps were used for hives, followed by log "gums." With these crude hives, it was difficult to know when the bees had problems with disease or starvation or if they were queenless; the beekeeper could not inspect the combs to determine what was wrong. By the same token, it was difficult to extract honey from these hives without damaging or destroying the bee colony. Typically, beekeepers had to kill their swarms each fall by burning sulphur at the entrance of the hive; then the honey and beeswax could be removed.

In the 17th and 18th centuries, beekeepers began to build movable-comb hives, which enabled them to inspect combs without damaging them. In 1789, Francis Huber invented the first movable-frame hive. The combs in this hive could be easily inspected like the pages of a book. In 1852, Lorenzo Langstroth, a minister from Pennsylvania, patented a hive with movable frames that hung from the top of the hive, leaving a 3/8-inch space between the frames and the hive body (the exact spacing at which bees will build comb they can move around, referred to today as "beespace"). By the turn of the 20th century, most beekeepers were using Langstroth's system. Langstroth is known as "the father of modern beekeeping."

Modern beekeeping methods evolved very rapidly following the invention of Langstroth's system. Wax-comb foundation, which made possible the consistent production of high-quality combs of worker cells, was invented in 1857. The centrifugal honey extractor was invented in 1865, enabling large-scale production of honey, and later in the century the radial extractor (where both sides of the frame are extracted at the same time) was invented. In 1889, G. M. Doolittle of New York developed the system for rearing queen bees that is still used today by all commercial queen-rearers. Bee smokers and veils evolved and improved. Also around this time, leaders in American beekeeping learned of the merits of the Italian honeybee, and they began to import these bees into the states. Today, the American version of the Italian honeybee is still widely used throughout the country.

The most significant advances in beekeeping are related to the areas of bee management and the extracting process. In general, the dimensions of hives and frames have become more standardized, drugs are available for disease control, artificial insemination of queen bees is being used commercially, and colony rental is being used increasingly for crop pollination. According to the National Honey Board, approximately 2.6 million colonies are rented for pollination annually.

In recent years, the commercial U.S. beekeeping industry has faced many challenges—ranging from the decimation of honeybee colonies by Colony Collapse Disorder and other diseases to foreign competitors that offer honey and orchard pollination services that are much less expensive than those offered by U.S. beekeepers.