The Humboldt penguin population at Peru's Punta San Juan Reserve has plummeted to fewer than 500 individuals by 2025. This collapse is the result of a lethal combination of avian flu outbreaks and severe El Niño weather patterns that decimated the region's seabird populations.
From 300,000 cormorants to a colony of 500
The scale of the decline at the Punta San Juan Reserve is staggering. As reported, the 133-acre peninsula once supported a massive ecosystem including 300,000 Guanay cormorants and over 250,000 other seabirds. By 2012, the area was a bustling hub of biodiversity where Humboldt penguins nested in guano deposits and cliff caves.
This crash is part of a broader, precarious trend for desert-dwelling species along the arid coasts of Peru and Chile. The loss of such a massive concentration of birds suggests a systemic failure in the local marine food web, turning one of the largest seabird gatherings on Earth into a graveyard of empty nests and skeletal remains.
How avian flu and anchovy depletion gutted the reserve
The biological collapse began in earnest during 2022 and 2023, when avian flu swept through the Punta San Juan Reserve. According to the report, the virus did not stop with birds; it jumped to marine mammals, killing hundreds of South American fur seals in a rapid transmission. This viral onslaught left the remaining population fragile just as a severe El Niño event began to warp the local environment.
El Niño raised sea surface temperatures in the eastern equatorial Pacific, forcing anchovies—the primary food source for Humboldt penguins—to move deeper and further offshore. This climate-driven food shrotage was exacerbated by industrial fishing operations, which competed with the penguins for the dwindling fish stocks. By July 2026, observers found only five penguins remaining in an area once teeming with life, with many breeding pairs abandoning their eggs to search for food.
Susana Cárdenas-Alayza and the guano-sack wall
Conservation efforts at the reserve are led by ecologist Susana Cárdenas-Alayza, who has managd the Punta San Juan Program for over two decades in collaboration with the Peruvian government, American zoos, and Cayetano Heredia University. The program utilizes artificial nests to protect chicks, but Cárdenas-Alayza has noted that diseases and climate events often escape scientific control.
The human element of the reserve adds another layer of complexity. Because the peninsula is a site for guano harvesting, workers have attempted to assist the birds. In the summer of 2025, workers constructed a half-kilometer-long wall made of guano sacks to shield Humboldt penguins during their arduous two-kilometer trek across the desert to reach the Pacific Ocean.. Despite these efforts, the sheer scale of the environmental pressure has overwhelmed local interventions.
The looming threat of a super El Niño
The colony now faces the prospect of a "super El Niño," which threatens to further disrupt the cold, nutrient-rich waters of the Humboldt Current. If sea surface temperatures continue to soar, the remaining population of fewer than 500 penguins may find it impossible to find enough prey to sustain a breeding cycle.
Several critical questions remain unanswered by the current reporting. It is unclear whether the Peruvian government intends to implement stricter industrial fishing quotas to protect the remaining Humboldt penguins, or if the avian flu has mutated into a permanent endemic threat in the region. Furthermore, the report does not specify if the "super El Niño" predictions are based on specific temperature thresholds or general climate modeling,leaving the exact timeline of the next threat ambiguous.
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