Ensconced in a plexiglass bubble some 500 feet beneath the azure waves of the southern Caribbean Sea, Carole Baldwin spied a lumpy oddball of a flesh-colored fish. It looked like an anglerfish, also known as a sea toad. Yet Baldwin, one of the most experienced Caribbean fish specialists alive, had not seen this variety.

She directed a technician in the five-person submarine to grab the creature with the vehicle’s suction arm. A squirt of anesthetic slowed the oddball so the arm could drop it into a milk crate strapped to the front of the sub.

Here, on one of 21 dives Baldwin and her colleagues made just off the island of Curacao, was another prize, another species probably new to science. Then the sub dropped. The groggy fish floated out of the crate, roused and wriggled off into the dark.

“There’s always one that gets away,” Baldwin said later in her office at the Smithsonian’s National Museum of Natural History, where a taxidermied swordfish presides from high atop the back wall. But at least a half-dozen newly discovered species did not escape the milk crate this summer.

At the surface, Baldwin photographed each fish and snipped tissue for DNA analysis, to see if the fish were indeed new to science, as she suspected.

While much of the ocean remains a vast unknown and no doubt full of unseen creatures, most of the Caribbean has been well surveyed. Pulling new species from this sea was “a huge surprise,” Baldwin said. “Everyone thought, ‘Been there, done that.’ ”

Baldwin is one of a handful of scientists exploring a little-studied twilight zone known as mesophotic, or “middle light,” reefs. Although they lie more than 200 feet below the surface, these reefs resemble their colorful, shallow-water cousins. Big barrel sponges, waving blue sea fans and soft yellow corals thrive, as do bright fish familiar to snorkelers whose rear ends poke above the waves.

“You could put somebody in a submarine, blindfold them, put them in front of a beautiful deep-reef environment and they wouldn’t know the difference,” Baldwin said.

A few intrepid explorers began diving down to deep reefs in the 1980s, most notably deep-scuba expert Richard Pyle in Hawaii. But only in the past few years have scientists such as Baldwin begun dipping into the twilight zone in earnest.

That’s because conventional scuba gear limits dives to 200 feet. And technology made famous by the deep-sea submersible Alvin in the 1960s allowed explorers to plunge to amazing depths, far beneath the twilight zone.

“If people come up with that kind of submersible money, they go right past this zone,” said Pyle, based at the Bishop Museum in Hono­lulu.

“We’re talking about areas that have never been looked at before, for the most part,” said Sylvia Earle, one of the world’s most prominent ocean advocates and an Explorer-in-Residence at the National Geographic Society. “The distance between 200 feet and 1,000 feet [deep] is perhaps the most neglected part of the ocean.”

Researchers need a ride

Baldwin’s voyage to Curacao began with a curious phone call in September 2010. “If you don’t have half an hour, don’t start talking,” said the voice belonging to Adrien “Dutch” Schrier, who owns a resort, an aquarium and a dolphin-encounter business on the island.

To his leisure empire, Schrier had added a $2.2 million submersible hardened to dive to 1,000 feet, bought from the Canadian company Nuytco. Schrier dubbed it the Curasub and began offering tourist excursions for $650. His resort happened to be situated perfectly: off the shoulder of South America, smack next to the continental drop-off. Motor just off Schrier’s pier, and the bottom plunges.

With a keen eye for fish — for his Seaquarium and for commercial sale — Schrier began noticing species he did not recognize. Through a contact, he found Baldwin and invited her down.

“Bad coffee, bad burgers, great diving,” Schrier told her.

So Baldwin, along with Ross Robertson from the Smithsonian’s Tropical Research Institute in Panama, launched the Deep Reef Observation Project. The goal: Cataloging the biodiversity of the twilight zone across the region.

Schrier offered sub rides to Baldwin’s crew gratis in May, June and July. It was a great deal, and not just for the price: Very few research submarines operate today.

Alvin, owned by Woods Hole Oceanographic Institute, is in dry dock for retrofitting. Earlier this year, the Harbor Branch Oceanographic Institute, part of Florida Atlantic University, disposed of two other workhorse vehicles, the Johnson-Sea-Links, with 9,000 dives between them. One is now mothballed, the other sold to Brazil. The National Oceanographic and Atmospheric Administration owns none, though it does fund work with two Pisces subs at the University of Hawaii.

“For the U.S., that’s about it,” said Earle. “It’s a disappointing gap.”

Schrier is eager to fill that gap. He purchased a mother ship for the Curasub from NOAA, the Chapman, which can drop the sub over twilight zones near Belize, Panama and elsewhere. Onboard, Baldwin and other researchers will be able expand their search for more of the Caribbean’s hidden biodiversity.

But first, they need funding: no more free rides from Schrier. Baldwin recently applied for a Smithsonian grant, hoping to get another shot at the ugly anglerfish that swam away: “We’ll be looking for that one next time.”

Hawaiian finds

Beyond the submersibles, there’s another option: deep-scuba diving. A self-described “fish nerd,” Pyle helped pioneer such dives in the 1980s. “My particular passion for fishes is finding new things,” he said, hours after disembarking from a month-long expedition to the Papahanaumokuakea Marine National Monument in the Northwestern Hawaiian Islands. “The best way to do that on the reef is to just go deeper than anyone had been before.”

So Pyle dives the twilight zone reefs, descending to 500 feet with a setup that recycles exhaled gas and uses exotic air mixes to prevent the bends. He has collected thousands of fish from across the Pacific and discovered more than 100 species. For each hour of bottom time — he gets only about 10 minutes at 500 feet — he finds 12 unknown species. “It’s an absolutely incredible rate of discovery,” said Earle.

In Hawaii, Pyle discovered a “dead zone” at about 200 feet, where temperatures fluctuate daily and limit the number of fish and coral species that can thrive.

Below that, where temperatures are more stable, the diversity of the reefs picks up again.

Few hard corals exist in the twilight zone, as they depend on symbiont microorganisms that need sunlight.

Fish colors differ, too. More than in the shallows, deep-reef fish tend toward red, which appears black in the depths. Black-looking fish can probably evade predators more easily, Pyle said. It may be that red is “physiologically cheaper” to make than black, he said, so fish have evolved with that color.

Also common are high-contrast color patterns, such as black-and-white, and red-and-white stripes. Pyle surmises that such patterns make it easier for mates to spot each other.

Pyle and a handful of other twilight zone researchers have just begun exploring one big question: Can the cooler deep reefs serve as a refuge for shallower species as the oceans warm? In 2007, NOAA gave Pyle a $250,000, five-year grant to explore the question.

For hard corals, which need light, the answer is no. For many fish, the answer may be yes. However, with so little research underway, it’s unclear if shallow-reef fish spawn progeny that migrate deeper, or if deep-bred juveniles migrate upwards. Pyle said a DNA-testing project he’s leading will help answer the question.

In the Northwestern Hawaiian Islands two years ago, Pyle and Randall Kosaki of NOAA found a twilight zone “nursery” teeming with juvenile fish.

The find highlighted a favorite message of Pyle’s: Conservation, which usually focuses on the shallow reefs, needs to be extended into the twilight zone. “The reef doesn’t end at 200 feet,” he said.