Scientists Capture First-Ever Photos of an Elusive “Beaked Whale” That Had Never Been Seen Alive

For years, a strange, repetitive clicking sound pulsed through the deep Pacific. It was heard again and again on hydrophones anchored to the seafloor or trailing behind research ships. Scientists gave it a name, or at least a placeholder: BW43. A code. A signature. Something out there, echolocating in the dark, but leaving no trace on the surface.

The North Pacific, especially the waters off Baja California, has long held secrets. It’s vast, deep, and unforgiving. Few things stay hidden for long in science, but beaked whales are an exception. They dive deeper, surface less, and avoid humans better than almost any other marine mammals. Some species remain known only from bones washed up on beaches.

BW43 lingered in datasets for over a decade. Some researchers suspected it came from one of the many species of Mesoplodon, a genus of beaked whales so poorly understood that even basic facts, how they look alive, where they go, are still debated. But without proof, guesses were all they had.

Now, that signal finally has a face. For the first time, researchers have directly connected BW43 to a living animal, photographed and genetically confirmed in the wild. The whale? Mesoplodon ginkgodens, also known as the ginkgo-toothed beaked whale. And this is the first time the species has ever been seen alive.

Connecting Sound to Species

The discovery didn’t happen overnight. A team led by researchers at the U.S. Naval Information Warfare Center Pacific spent years preparing, sailing to the same remote region each summer. They towed listening arrays behind a ship, used raised viewing platforms, and waited.

In 2024, their efforts paid off. The team recorded 21 BW43 detections and observed five groups of beaked whales in the same general area. One juvenile male approached the research vessel close enough, about 20 metres, for the scientists to collect a small skin sample using a crossbow dart. Genetic analysis confirmed the sample belonged to Mesoplodon ginkgodens, linking the species with the BW43 signal for the first time.

Alongside the biopsy, the team gathered environmental DNA (eDNA) from seawater. These genetic traces, left behind as whales move through the ocean, also matched M. ginkgodens. High-resolution photographs captured defining physical traits: pale facial markings, a dark eye patch, and the beginnings of tusk eruption in the juvenile.

None of these alone were enough. But together, genetics, photos, and simultaneous acoustic detection, they built a strong case. The signal had a source. And the whale, once known only from strandings, had finally been observed alive.

A Life Lived Far Below the Surface

This whale, like others in its genus, is a master of staying out of sight. Beaked whales are known for their exceptional diving performance. A 2006 study in the Journal of Experimental Biology documented dives in related species reaching depths beyond 1,800 metres, with foraging dives lasting nearly an hour.

They surface briefly, breathe a few times, and vanish again. They don’t approach ships. They don’t linger near coastlines. That’s part of why BW43 went unidentified for so long. The whales spend most of their lives out of reach — acoustically present, but visually invisible.

During the survey, researchers photographed adult males bearing long white scars, likely from intraspecific combat using their tusks. These flat, leaf-shaped teeth appear near the tip of the snout and are used not for feeding but fighting. Circular scars from cookiecutter shark bites were also common, a reminder of the predation risk even in deep water.

Most of the sightings occurred over the continental slope, between 861 and 2,199 metres in depth. That habitat, combined with the species’ behaviour, explains why it had remained undocumented in the wild for so long. It also suggests the whales may be more resident to the area than previously believed.

What This Means for Marine Monitoring

Now that researchers know what BW43 represents, they can begin using acoustic monitoring to track M. ginkgodens across the North Pacific. Networks of hydrophones on the seafloor, towed by vessels, or attached to drifting buoys can detect the click trains that make up the BW43 signal, even when the whales are too far or too deep to observe directly.

Because beaked whales have shown sensitivity to naval sonar, this identification helps in more than just ecological mapping. It allows both environmental regulators and naval operations to avoid acoustic overlap with known habitats. Sound, in this case, becomes a tool for protection.

Previous mass strandings of beaked whales have occurred following sonar exercises. A 2014 study in Frontiers in Physiology examined how mid-frequency sonar may alter deep-diving behaviour in whales and potentially contribute to gas embolism events. With M. ginkgodens now traceable through sound, future mitigation can be better targeted.

The team’s approach — combining real-time audio tracking, visual confirmation, genetic sampling, and eDNA — offers a new model for attributing other unidentified sonar signals. For example, the BW37V signal, once unattributed, was later associated with Hubbs’ beaked whale in a separate acoustic identification study. Similar work is still needed for signals like BW29.