Beekeepers Lost 62 Percent of Their Colonies. USDA Just Lowered the Bar for 'Normal.'

Every February, roughly a third of the country's managed honeybee colonies get loaded onto flatbed trucks and driven to California to pollinate 1.4 million acres of almonds — the single largest paid pollination event on Earth.▸ In the season that ended that migration in 2025, commercial beekeepers who make their living trucking bees to jobs like that one lost 62.3% of their colonies between June 2024 and March 2025, the worst loss rate ever recorded by either of the two industry surveys that measured it — surveys co-authored by USDA's own bee researchers, posted to bioRxiv in August 2025. Two years later, almost to the day, USDA published a rule rewriting the technical line that decides how much of a loss like that the federal government will actually pay for.

USDA's own colony census backs up what beekeepers were reporting.▸ The country's managed colony inventory (operations with five or more hives) fell to 2.63 million on January 1, 2025, down 1% from a year earlier, and the fourth quarter of 2024 alone destroyed 403,270 colonies — 14% of the fleet, the worst single quarter USDA tracked all year, according to USDA NASS's Honey Bee Colonies report (released Aug. 1, 2025). Losses specifically bearing the fingerprint of Colony Collapse Disorder — no dead-bee buildup, a vanished adult population, food reserves left untouched — hit 148,410 colonies in the first quarter of 2025, up 110% from the same quarter in 2024. Varroa mites, the parasite most beekeepers blame first, were reported on nearly 30% of colonies in every quarter surveyed.

Two industry-run surveys tried to size the damage precisely.▸ Project Apis m. and the American Beekeeping Federation — with USDA-ARS scientists as co-authors — polled beekeepers managing over half the country's colonies and found commercial operations (over 500 hives) lost significantly more than smaller-scale keepers, a reversal of the usual pattern, in results posted as a preprint in August 2025. Separately, the Apiary Inspectors of America and Auburn University's long-running U.S. Beekeeping Survey found a national annual loss rate of 55.6% for April 2024–April 2025 — also the highest since that survey began in 2010-11.

The commercial operators who lost the most are also the ones the almond bloom depends on: an estimated 1.15 million colonies were lost among just the 280 commercial respondents to the Project Apis m. survey alone — out of roughly 1,600 commercial beekeeping operations nationwide that, per USDA-cited industry estimates, produce 60% of the country's honey and supply most of its paid pollination.

The federal government's honeybee safety net doesn't pay for ordinary losses — only for losses in excess of a threshold FSA calls the "normal mortality rate."▸ A beekeeper who loses 40% of their colonies in a bad year, with the threshold set at 24.2%, gets compensated only for the 15.8 percentage points above that line, at a minimum of 75% of that year's government-set fair market value per colony (90% for beginning, veteran, or socially disadvantaged producers), under the Emergency Assistance for Livestock, Honeybees, and Farm-Raised Fish Program (ELAP), per FSA's 2024 ELAP honeybee fact sheet. That fair market value was set at $129 per colony for 2024 — up from $60–70 per colony when ELAP began, in FSA's original October 2011 fact sheet.

The threshold itself has moved a lot more than most people paying attention to bee die-offs would guess:

From 2011 to 2024, FSA recalculated the rate every year from published mortality data — and as the industry's baseline die-off rate climbed, so did the bar a beekeeper had to clear before any payment kicked in.▸ On July 9, 2026, USDA published a rule in the Federal Register implementing Section 10401(c) of the One Big Beautiful Bill Act, signed a year earlier, that ends the year-by-year calculation and fixes the rate at a flat 15% "for program year 2026 and subsequent years." It is, on its face, a lower bar — more of a beekeeper's loss now counts as compensable than it would have under 2024's 24.2% line. It is also a rule that arrives a full year after the worst die-off on record, applies only to losses going forward, and leaves the 2024-25 crisis assessed against the threshold FSA had already set before anyone knew how bad that winter would be.

What ELAP actually pays out, meanwhile, is modest against the scale of the problem.▸ Honeybee assistance averaged $45 million annually from 2020 to 2022, nearly all of it — 95% — for colony losses rather than hive or feed damage, according to USDA's Economic Research Service.

Against a die-off that killed an estimated 1.1 million-plus colonies in a single nine-month stretch, a $45 million annual program — even paid out in full, which payment-limitation and eligibility rules ensure it isn't — covers a fraction of what beekeepers actually lost.

The bee shortage shows up most clearly where the money actually changes hands: the price growers pay to rent colonies.▸ In California's Central Valley, almond growers paid an average of $209 per colony in 2025, up 15% from $181 in 2024 — even as the number of colonies they were able to rent fell to 1.63 million, down from 1.8 million the year before, according to USDA NASS's Cost of Pollination report (released Feb. 13, 2026, covering Arizona, California, and Hawaii — USDA's "Region 6 & 7"). Growers paid more, for fewer bees, and the total dollars spent on almond pollination in that region still rose to $340.7 million, from $325.8 million the year before.

The price held roughly steady through the years the industry could absorb ordinary attrition — $194 in 2022, $188 in 2023, $181 in 2024 — then jumped the year after the worst die-off on record thinned the number of colonies healthy enough to survive a truck ride and a bloom.▸ California's own in-state numbers show the strain of assembling that fleet directly: the state started 2025 with 910,000 colonies, then swelled to a peak of 1.26 million as beekeepers trucked colonies in from other states for almond bloom — and still lost 83,000 of them, 7%, before the quarter was out, per USDA NASS. Every dollar of that $15-per-colony jump is a cost a fruit-and-nut buyer eventually pays, and none of it flows through ELAP, which pays beekeepers directly for dead colonies, not growers for the price of live ones.

Colony-loss figures combine independently conducted surveys — Project Apis m./American Beekeeping Federation (with USDA-ARS co-authors) and the Apiary Inspectors of America/Auburn University — covering overlapping but not identical time windows and beekeeper samples; loss rates are self-reported and weighted per each survey's own published methodology. ELAP payment-rate and fair-market-value figures describe the honeybee colony-loss category specifically, not hive or feed losses, which are paid on separate schedules.