Blue whales have gone missing off the Galápagos. Scientists think El Niño could be why.

For nine months, a scientific expedition searched for blue whales in the waters around the Galápagos Islands but found none. Between October 2025 and July 2026, the researchers surveyed areas of the Ecuadorian archipelago where the giants had historically been recorded, hoping to attach satellite tags and learn more about the animals’ migratory routes. The search ended without the team tagging a single whale.

The absence coincided with unusually warm ocean conditions during an El Niño event. Sea surface temperatures were as high as 82 degrees Fahrenheit (28 degrees Celsius), while at a depth of 330 feet (100 meters) water temperatures ranged from 66 to 67 F (18.9 to 19.4 C) — up to 9 F (5 C) warmer than usual for that time of the year.

This raised the possibility that El Niño changed where blue whales were finding food and, in turn, where they went. The researchers suspect the animals may be seeking colder, more productive waters. However, the whales themselves are still missing.

“The hypothesis is that the whales are staying in areas with greater productivity [more food] farther south, in waters with slightly cooler temperatures,” Daniela Alarcón, the expedition’s leader and a researcher at the Universidad San Francisco de Quito’s Galápagos campus and the Galápagos Science Center, told Live Science.

As to where the missing whales have gone, possibilities include the waters off Peru and offshore areas where the animals could go undetected. In this scenario, the unusually warm waters around the Galápagos Islands would act as a “temperature barrier,” Alarcón said, preventing them from feeding in the archipelago’s waters.

Why water temperature matters

Blue whales (Balaenoptera musculus) can consume up to 12,100 pounds (5,500 kilograms) of krill — small crustaceans that make up the whales’ primary food source — every day. That means they need to find areas with enough food to sustain them.

“These are very large animals that need to move to areas where they can keep feeding,” Alarcón said.

It’s not yet clear whether this year’s El Niño caused a krill shortage in the waters off the Galápagos, but some indirect evidence points that way.

Past expeditions suggested that blue whales tend to feed in water layers around 71 F, which this season was identified around the Galápagos at a depth of about 197 feet (92 m). By contrast, peak chlorophyll concentrations, an indirect indicator of abundance of the krill’s food source, phytoplankton ‪—‬ were recorded much higher in the water column, at between 39 and 121 feet (12 to 37 m) below the surface. Because krill abundance wasn’t directly measured, that data suggests, but does not establish, that there was a mismatch between the whales’ preferred feeding layer and the presence of their food.

“Honestly, we had never encountered such unusual conditions before,” Juan Pablo Muñoz, a marine biologist at the Universidad San Francisco de Quito who was also on the expedition, told Live Science.

Continuation of a trend

The whales’ absence did not come as a complete surprise to the team. Sightings had already begun to decline before the most recent expedition. Reports submitted through Cetácea Galápagos, a citizen science network, began to dwindle between August and September 2025. There were two isolated reports of blue whales, in May and June 2026, but the team could not confirm either one, despite intensifying its search.

“We knew conditions wouldn’t be the same, but we thought that if we put in more effort, we might be able to find some individuals. But we searched, and searched, and searched — and found nothing,” Alarcón recalled.

Part of that could be down to the elusive nature of the giant creatures. Humpback whales (Megaptera novaeangliae)are generally easier to spot, Muñoz noted. In some places, they can be seen from the shore or after a half-hour boat ride. Blue whales, by contrast, rarely approach mainland Ecuador’s coast and tend to stay far from populated areas in the Galápagos.

Sensitive to temperature fluctuations

Fernando Félix, a marine biologist at the Pontifical Catholic University of Ecuador who was not part of the expedition, was unsurprised by the result.

“We already knew there wouldn’t be any blue whales in the Galápagos,” said Félix, who is also a researcher at the Whale Museum (Museo de Ballenas).

Félix told Live Science that there are historical precedents for this behavior in the southeastern Pacific. During the 1982-1983 El Niño, which also brought substantial ocean warming, blue whales and other species, including fin whales (Balaenoptera physalus) and Bryde’s whales (Balaenoptera brydei), were recorded shifting southward.

“We might think that because they are ‘just animals,’ they lack memory or don’t understand these processes — but we would be wrong,” Félix said. “They can clearly sense that when temperatures are unusually high as they travel north from the south, vertical mixing has been disrupted and there is no food in the Galápagos. They perceive environmental conditions and naturally direct their movements toward areas where they believe feeding conditions are better.”

Rather than indicating a mass die-off, the whales’ disappearance may reflect a shift in their movements in response to changing ocean conditions, Félix said.

“I don’t think the whales have died,” Felix said. “They simply didn’t go to the Galápagos region. They went elsewhere, where conditions were better.”

This response to environmental conditions may also have impacted dolphin movements. Pods may have moved toward colder waters, where food could be more abundant, or may have even dispersed, Félix suggested.

When will blue whales return to the Galápagos?

El Niño’s effects will likely persist over the coming months. “Between January and May 2027, we’ll have warm water coming from the north and warm water coming from the west,” Félix warned. “This is going to hit us extremely hard.”

Blue whales, humpback whales and dolphins would likely return to Galápagos waters once El Niño subsides and ocean conditions begin to normalize. He said pelagic fish (species that live in the water column rather than on or near the seafloor) ‪—‬ including tuna, swordfish, anchovies and sardines, which have also moved toward colder waters ‪—‬ would return as well.

Muñoz agreed. Krill populations can rebound just one to three months after cold, nutrient-rich waters begin to rise to the surface. More whale sightings were recorded in the years following the 2015 and 2023 El Niño events. Based on these precedents, he suggested that 2028 could be a promising year if cold water returns to the surface. “The system bounces back,” he said.

Félix compared El Niño to a computer restart. “It resets the environment, allowing ecological processes to begin again,” he said. He’s confident that blue whales will return to the area. “I can guarantee that there will be large numbers of blue whales at this time in 2028,” he told Live Science.

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