What Do Whale Sharks Eat When We’re Not Watching?

Picture a whale shark feeding at the ocean’s surface. Its enormous mouth opens wide as it moves through the water, filtering vast quantities of seawater in search of some of the ocean’s smallest inhabitants.

It is an image that has come to define the world’s largest fish.

At seasonal feeding grounds around the world, whale sharks gather where food is abundant, offering scientists a rare opportunity to observe these otherwise elusive ocean giants. Here, researchers have watched them feeding on dense concentrations of zooplankton, including tiny crustaceans such as copepods.[1]

But there is a problem.

We can only observe a fraction of their lives.

Once a whale shark leaves the surface and disappears into the blue, following it becomes considerably more difficult. Much of what we understand about whale shark feeding ecology has therefore been pieced together from surface observations, samples of the plankton surrounding feeding sharks, and indirect clues such as stable isotopes and fatty acids.[2]

What they eat when we are not watching is much harder to uncover.

Now, a study published in the Journal of Fish Biology has offered scientists a rare glimpse beneath the surface.

Researchers used DNA recovered from the stomach contents of a juvenile whale shark from the Gulf of California, Mexico, to identify traces of the organisms it had consumed—the first direct dietary assessment of a juvenile whale shark using this technique.[3]

Some of what they discovered was exactly what we might expect.

Some of it was not.

And hidden among those fragments of DNA were clues suggesting that the feeding life of the world’s largest fish may be more complex than we realise.

The Gentle Giant — and the Diet We Thought We Knew

Despite belonging to a family of animals often associated with powerful predators, whale sharks (Rhincodon typus) are filter feeders.

Rather than hunting large prey, they feed by drawing huge volumes of seawater into their mouths and passing it across specialised filtering structures. Water escapes through the gills, while tiny organisms suspended within it are trapped and swallowed.[1]

Their menu can include zooplankton, copepods, krill and other small crustaceans, as well as fish eggs and other small organisms carried within productive waters.[1,4]

For a fish that can grow to more than 12 metres in length, some of its most important prey can therefore be remarkably small.

This is particularly visible at whale shark aggregation sites.

In places where currents, seasonal productivity and spawning events create dense concentrations of food, whale sharks can gather in significant numbers. These predictable feeding events have given researchers extraordinary opportunities to study the species—and have helped shape much of our understanding of what whale sharks eat.[2]

One of these places is the Gulf of California.

In the Bay of La Paz, juvenile whale sharks regularly gather in productive coastal waters where zooplankton—particularly copepods—can occur in high concentrations.[3] Watching these enormous sharks feeding amongst clouds of tiny prey seems to tell a straightforward story:

Find the plankton, and you find the whale sharks.

But whale sharks do not spend their entire lives feeding at the surface.

They travel through vast stretches of ocean and move vertically through the water column, spending periods of time far beyond the environments where we can easily observe them.[5]

And that creates an important gap in our understanding.

The feeding behaviour we witness at the surface may tell us what whale sharks eat when we can see them.

It does not necessarily tell us everything they eat when we cannot.

A Different Way of Looking at Dinner

To uncover what a whale shark has been eating, researchers face an obvious challenge: by the time food reaches the stomach, much of it no longer looks like food.

Soft-bodied organisms can break down quickly, while tiny prey may become fragmented beyond recognition. Traditional stomach-content analysis relies on physical remains that scientists can identify—something that becomes much harder when those remains have already been partially digested.[3]

This is where DNA metabarcoding can reveal clues that the eye cannot.

Instead of asking “What can we recognise?”, researchers look for traces of genetic material left behind by the organisms that have been consumed.

DNA is extracted from a sample and particular genetic sequences are analysed. These sequences can then be compared with reference databases to help identify the groups of organisms they came from—almost like searching for biological fingerprints left behind after a meal.[3]

SCIENCE, EXPLAINED

DNA metabarcoding allows scientists to identify many different organisms within a mixed sample using traces of their DNA.

For this study, researchers analysed the stomach contents of a juvenile whale shark from the Gulf of California, Mexico, targeting a region of the 18S ribosomal RNA gene to investigate the diversity of organisms present.[3]

The technique revealed an extraordinary mixture of life.

After filtering the results to focus on potential prey, the researchers identified 129 distinct prey-associated DNA sequence variants, spanning a range of taxonomic groups.[3]

It was a rare molecular snapshot of a meal that could otherwise have been extremely difficult to reconstruct.

And when the researchers began looking at which organisms those genetic traces belonged to, one part of the menu was immediately familiar.

The Expected Discovery: Tiny Crustaceans

Among the DNA recovered from the whale shark’s stomach were traces of a familiar food source: copepods.

These tiny crustaceans are among the most abundant animals in the ocean and form an important link in marine food webs, transferring energy from microscopic producers to much larger animals—including the world’s largest fish.

In the study, Hexanauplia—a group represented by four orders of copepods—accounted for 40.2% of the prey DNA reads identified.[3]

Their presence was not particularly surprising.

Copepods are already known to be an important part of the whale shark diet, and dense concentrations of them are associated with the seasonal gatherings of juvenile whale sharks in the Bay of La Paz.[3]

In other words, the DNA was confirming part of the story scientists already knew.

But another group appeared in even greater abundance.

And this time, the researchers were not expecting it.

Then the DNA Revealed Something Unexpected

Among the prey DNA detected, the largest proportion did not come from copepods.

It came from Anthozoa—a group of marine animals that includes corals, sea anemones and sea pens.

Anthozoan sequences accounted for 43.4% of the prey DNA reads identified, with the study detecting groups that included soft corals and sea pens.[3]

For an animal we so often picture feeding on clouds of plankton near the ocean’s surface, this was an intriguing result.

Unlike the copepods detected alongside them, many anthozoans are benthic organisms, living attached to or closely associated with the seafloor. Sea pens, for example, are colonial animals commonly found anchored within soft sediments, while soft corals are also associated with benthic habitats.[3]

Their DNA inside the stomach of a whale shark therefore raised an unexpected question:

Where—and how—had this shark encountered them?

The discovery does not yet provide a definitive answer.

But it offers a tantalising clue that the feeding ecology of whale sharks may extend beyond the plankton-rich surface waters where we most often witness them feeding.[3]

A Clue From Deeper Water?

The presence of soft coral and sea pen DNA becomes particularly interesting when we consider where these animals live.

Unlike the plankton concentrated in surface waters, many anthozoans are associated with the seafloor. Their appearance in the stomach contents therefore raises the possibility that this whale shark had encountered food resources connected to deeper or benthic habitats.[3]

And there is reason to take that possibility seriously.

Although whale sharks are frequently encountered near the surface, tracking studies have revealed a very different world beneath the one we can see. These sharks are capable of travelling through an enormous vertical range, making dives hundreds—and sometimes more than a thousand—metres below the surface.[5]

There is also growing evidence that whale sharks do not restrict their feeding behaviour to the upper ocean. Researchers have documented individuals appearing to feed close to, and even directly from, the seafloor.[6,7]

The new DNA evidence adds another intriguing piece to that puzzle.

It does not tell us exactly where the juvenile in this study consumed the anthozoans, nor does it prove that whale sharks routinely target them in deeper water. But it raises the possibility that some feeding may take place in environments we rarely witness.

For researchers, that matters.

Our understanding of whale shark feeding has inevitably been shaped by the places where these enormous animals are easiest to find and observe. Surface aggregations provide an extraordinary window into their lives—but they are still only a window.

What we see at the surface may only be part of the story.

Does This Mean Whale Sharks Eat Coral?

It is the obvious question.

If researchers found soft coral and sea pen DNA inside a whale shark’s stomach, does that mean whale sharks are actively seeking out and eating them?

Not necessarily.

DNA metabarcoding can tell researchers that genetic material from these organisms was present, but it cannot reconstruct exactly how it got there.[3]

The anthozoans may have been consumed directly. They may also have been ingested incidentally while the shark was feeding on other organisms nearby, or their DNA could have entered the food chain through prey that had themselves consumed anthozoan material.[3]

There is another important limitation.

The 43.4% figure refers to the proportion of prey DNA reads detected, not the physical proportion of the shark’s meal. DNA metabarcoding is extremely useful for revealing which organisms are present, but the number of DNA sequences recovered does not translate directly into the amount of each organism that was eaten.[3]

So we cannot say that 43.4% of this whale shark’s diet was coral.

What we can say is that the amount and diversity of anthozoan DNA detected was unexpected—and significant enough to raise new questions about where and how this individual had been feeding.

Rather than providing a simple answer, the discovery has opened another door.

Were these organisms deliberately consumed? Were they encountered while feeding near the seafloor? Or is there another connection within the food web that we do not yet understand?

For now, we don't know.

And that uncertainty is an important part of science. A discovery does not always give us an answer.

Sometimes, it gives us a better question.

One Shark, Not an Entire Species

There is another important piece of context to keep in mind.

This study examined the stomach contents of one juvenile whale shark.[3]

That makes the findings fascinating—but it also means they cannot tell us what every whale shark is eating.

Whale sharks are highly mobile animals found across tropical and warm-temperate oceans. Their diet can vary depending on where they are, which prey are available and the feeding opportunities they encounter. A juvenile feeding in the Gulf of California may therefore have a very different menu from a whale shark gathering around a fish-spawning event elsewhere in the world.[2,4]

The researchers describe their findings as an important expansion of the known diversity of potential whale shark prey—not as a complete picture of the species’ diet.[3]

More individuals will need to be studied before scientists can determine whether the unexpected prey detected here represents an unusual meal, a local feeding strategy, or something occurring more widely among whale sharks.

But that is exactly what makes this study so interesting.

Science often advances through observations that challenge what we expect and give researchers something new to investigate.

One shark cannot tell us everything about its species. But sometimes, one shark can give us an entirely new set of questions to ask.

Why Understanding Diet Matters for Conservation

Understanding what an animal eats tells us much more than what is on its menu.

It can reveal where it finds food, which habitats it relies upon, how it interacts with other species and where it sits within the wider marine food web.

For whale sharks, these questions are particularly important.

The species is currently classified as Endangered on the IUCN Red List, with threats including fisheries interactions, vessel strikes and other human pressures.[9] Protecting whale sharks therefore requires scientists to understand not only where these animals travel, but what draws them to particular environments along the way.

We already know that productive feeding grounds can be incredibly important. Seasonal blooms of plankton, fish-spawning events and concentrations of other prey can attract whale sharks to particular areas—sometimes bringing large numbers of individuals together.[2,4]

But the DNA recovered in this study reminds us that the habitats we associate most strongly with whale shark feeding may not tell the whole story.

If future research finds that whale sharks regularly obtain food from deeper or benthic environments, it could broaden our understanding of the habitats and food-web connections that support them throughout their lives.[3]

This single study cannot tell us which additional habitats require protection, nor can it establish how common this type of feeding might be.

What it can do is reveal another piece of a much larger puzzle.

Because to protect an animal that can disappear across vast oceans and descend far beneath the surface, we first need to understand how it uses the ocean—even in the places where we cannot follow.

The Ocean Still Has Secrets

Whale sharks are among the most recognisable animals in our ocean.

We know they can cross vast distances, dive deep beneath the surface and return seasonally to feeding grounds around the world. We have watched them gather where plankton blooms, followed their movements by satellite and studied the chemical signatures preserved within their tissues.

And yet, there is still so much we do not know.

This study offers only a snapshot—the stomach contents of a single juvenile whale shark at one moment in its life.[3]

But within that snapshot were traces of animals scientists did not expect to find.

Soft corals. Sea pens. Tiny fragments of DNA pointing towards parts of the whale shark’s feeding ecology that remain largely hidden from us.

Perhaps future studies will reveal that these organisms are regularly consumed. Perhaps they will uncover feeding behaviours we have rarely witnessed. Or perhaps the explanation will be something entirely different.

That is what makes discoveries like this so exciting.

The ocean still contains behaviours, relationships and entire chapters of animal lives that we have never seen.

Even the world’s largest fish can disappear beneath the surface and leave us wondering what it is doing down there.

One stomach. Traces of DNA. And an entirely new set of questions about what the world’s largest fish is doing beneath the surface.

The more we learn about the ocean, the more it reminds us how much there is still left to discover.

References

[1]

Motta, P. J. et al. (2010).

Feeding anatomy, filter-feeding rate, and diet of whale sharks Rhincodon typus during surface ram filter feeding off the Yucatan Peninsula, Mexico.

Zoology, 113(4), 199–212.
Read the publication → https://doi.org/10.1016/j.zool.2009.12.001

[2]

Rohner, C. A. et al. (2013).

Diet of whale sharks Rhincodon typus inferred from stomach content and signature fatty acid analyses.

Marine Ecology Progress Series, 493, 219–235.

Read the publication → https://doi.org/10.3354/meps10500

[3]

García-Baciero, A., Mac Loughlin, C., Ramírez-Macías, D. & Munguia-Vega, A. (2026).

Unveiling the whale shark diet: Insights from stomach content DNA metabarcoding.

Journal of Fish Biology, 1–7.

Read the publication → https://doi.org/10.1111/jfb.70534

[4]