When a BBC team was despatched to find new marine species in Micronesia, the trip gave Kate Humble the chance to dive in some of the world's most spectacular underwater environments

Chuuk Lagoon is a long way away. From anywhere. Which makes it all the more extraordinary that it should have been the setting for one of the most comprehensive defeats of the Second World War. In February 1944, the Americans launched Operation Hailstone, a two-day mission to wipe out the Japanese naval fleet, which was hidden in this distant Pacific atoll. It was a success; so much so that many historians see it as the turning point of the war in the Pacific. It also means that beneath the waters of Chuuk Lagoon are the wrecks of more than 70 ships and planes, making it a must-visit place for divers – and the ideal starting point for a new BBC expedition.

Back in April last year, 28 people, including some of the best underwater cameramen and deep-water biologists in the world, flew in from all corners of the globe, along with five tons of diving and filming equipment, six jars of Marmite and a crate of English Breakfast tea. Our mission: to travel the length of Micronesia and search for new animal species in waters where few people, if any, have dived before. But our journey would also take us to some of Micronesia's better-known treasures, places where I, like any keen diver, had long wanted to go.

We were supposed to go straight to the port and meet the boat which would be our home for the next five weeks, but it had been delayed by bad weather. So the expedition began with no boat and tsunami warnings being broadcast on the radio. We found a hotel, filled the conference room with our bewildering array of crates and boxes and prepared to go diving anyway.

My first dive was on the wreck of a supply ship called the Fujikawa Maru. The most startling thing as we started our descent was the clarity of the water. The deck, 16 metres below, was as visible as if it had been above the surface.

Heavily encrusted with an astonishing array of hard and soft corals, sponges, clams and feather stars, the ship provoked conflicting emotions. It is, like all the other wrecks at Chuuk, a war grave, a site where hundreds of people lost their lives. Despite spending more than 60 years beneath the surface of the sea, it is also surprisingly intact, which makes it all too easy to imagine the terror of those living and working on it when it was struck. However, the haunted sensation I had as I moved slowly over the deck and down into the hold to inspect the remains of an aircraft was tempered by the fact that I was surrounded by crowds of vibrant, colourful life.

Shoals of reef fish gathered among the waving arms of the corals and fans, or patrolled the decks like well-drilled soldiers. Squadrons of jacks cut through the water in tight formation and crinoids reached out from their perches with long, feather-like tentacles as we drifted past. After an hour we surfaced. The bleariness of our jet lag had gone,

replaced by an overwhelming desire to get underwater again as quickly as possible.

Mike Pitts, the cameraman I was working with, knows Chuuk well and was keen to make our next dive on the huge Shinkoku Maru. This vast hulk of a ship is more than 100 metres long and lies upright in just over 30 metres of water, its anchor chains transformed into decorated columns by hundreds of giant clams. The bridge, too, is still clearly visible, with the ship's telegraph and compass in place. We dived to it several times, at night as well as during the day, and it is probably one of the most atmospheric of all of Chuuk's shallower wrecks. We drifted down to a lower deck and made our way through an open door into a low-ceilinged room, trying hard not to stir up the thick layer of sediment that covered the floor. In the sharp beam of our lights we made out a table, and on it bottles and jars. This had been the ship's operating theatre, and on the table, in a careful pile almost like a mountain cairn, was a small heap of human bones. I had thought that all the human remains had been recovered and given a proper Japanese burial, but Mike said that divers still occasionally discover these stark reminders of the cost of war.

The Shinkoku, like the Fujikawa, is also a haven for marine life of all shapes and sizes. In the middle of one of the decks is a batfish cleaning station. Here batfish, curious-looking square fish, also known as spade fish, queue up to have parasites and any unsightly flaky bits removed by helpful little stripy fish called cleaner wrasse. It's a sort of piscatorial car wash. We loitered on the outskirts, but the batfish proved rather coy about being filmed performing their ablutions and it took several attempts to get the footage we wanted. Finally we were rewarded by a shameless batfish who hung upside down with an ecstatic expression as cleaner wrasse darted in and out of its gills and over its body.

News arrived that our ship, the Big Blue Explorer, had finally arrived in port. We now had the task of packing up everything we'd unpacked, loading it on to a series of flatbed trucks and unloading it again at the other end, all in the treacly humidity that is Chuuk's climate. As we were hauling crates and wiping sweat out of our eyes we all began to fear that the Big Blue might not be big enough. But we did fit, just, and after a final, spectacular night dive where underwater cameraman Mike deGruy co-ordinated the entire camera team to light up the Shinkoku's bridge, we set sail on the first leg of our epic sea journey.

We were heading for Yap, another divers' favourite and the midpoint between Chuuk and our final destination, Palau.

On the way to Yap are several small atolls and submerged pinnacles, all of which made our team of deep-water ichthyologists, led u o by Richard Pyle, very excited indeed. Richard, John and Brian are "rebreather" divers, which means they use a form of diving equipment where exhaled gas is recycled. They can stay underwater for much longer than is possible with normal scuba kit, and think very little of diving to depths of 100 metres and more in the pursuit of new species.

Their ideal dive site is a wall or a drop-off with no current and great visibility. They found all of those things at Poluwat, Grey Feather Bank, Fais and Ulithi, places where it is highly probable that no one has ever dived before. I hung about in the shallows, astounded by visibility of more than 100 metres but disappointed by a lack of big, charismatic species such as rays and sharks. No such qualms from the Fish Nerds, as they were affectionately known. They came up from every dive, having endured four or five hours of decompression with their buckets full of fish, each time announcing that they had just had the dive of their life.

As a result of their efforts, more and more fish ended up pinned on to polystyrene boards waiting to be photographed and identified. It might seem shocking that it was necessary to pluck these fish from the sea, but to ascertain properly whether something is a new species, to classify and describe it, you need an actual specimen, not just a photograph. Everything from skeleton to scales to internal organs and DNA was studied back in the lab in Hawaii – and many of the fish proved to be previously undescribed and unknown to science. Our mission to discover new species was proving fruitful.

Less fruitful were our initial attempts to capture on film Yap's main attraction: manta rays. These vast plankton-eaters are related to sharks and look like stealth bombers. They are high on any diver's list of dream encounters. Yap has well-known, accessible sites where, according to Bill Acker – a large, friendly Texan who runs a local hotel and dive centre – sightings are more or less guaranteed.

Never, ever, say that to a film crew. It is the kiss of death. Bill took us to a sandy-bottomed channel where mantas were said to queue up in an orderly fashion, like the batfish in Chuuk, to be cleaned. Hour after hour we lay on the bottom, fingers wedged in the sand so we didn't get swept away by the current, just waiting. Nothing. As our air supplies ran low, we would return to the boat, and after an hour or so would try again. No joy. At dusk, to lift our spirits we went in search of mandarin fish. These highly patterned little jewels appear in shallow reefs after dark and are another Yap favourite. Our team went in, lights blazing, cameras at the ready and the mandarin fish, sensibly, stayed hidden in the coral. By contrast, tourists diving a different bit of the reef saw loads.

Clearly we needed to be a bit more subtle in our approach, so we scaled down operations and went back to try to find the mantas. As we finned down the channel, Bill pointed upwards. Above us was the unmistakable outline of a manta ray, well over two metres across, hovering in the current with the effortless grace of a bird of prey riding thermals. We stayed as long as our air supply would allow, as a series of these graceful giants passed only centimetres above our heads and hung almost motionless in the current to allow the cleaner wrasse to get to work. Flushed with success, Mike Pitts and I went back to the shallow reef that evening with just one camera and a small light and spent two enchanting hours in the company of several pairs of mandarin fish, feeding, flirting and courting amongst the branches of their impenetrable coral forest.

Palau's jellyfish aren't nearly so tricky. After a sea crossing rough enough to throw the furniture around the boat and make me take to my bunk, put a sheet over my head and pray for dry land, we reached our final destination, perhaps the most beautiful of all the places we'd seen. Palau is made up of three large thickly forested islands and hundreds of smaller coral islets that stick out of the sea like bright-green mushrooms. Exploring the rock islands by kayak is one of Palau's many treats. The water is so clear you don't need a mask and snorkel to see the fish; the wild tangle of vegetation that covers the islands is home to giant fruit bats and any number of birds. In the middle of one of these islands is a saltwater lake, fed by seawater percolating through the porous coral. In it is a species of jellyfish found nowhere else in the world, and they are there in their millions. They have few predators so they have lost the majority of their stinging cells. Swimming with them is safe.

When we arrived, the sun was on the opposite end of the lake from the jetty and there was not a jellyfish to be seen. "Just you wait," said Mike as we got in and started to fin towards the sun. Suddenly, I saw one: a gelatinous, pinky-orange orb about as big as my hand. Then I saw another, and another, and I realised that all I could see was jellyfish. I was looking at a wall of them, a great pulsating mass that parted as I swam through them and closed up again behind me. Mark, our sound recordist, said it was like being in a giant screen-saver – mesmerising, hypnotic, strange and wonderful. We emerged, unstung and wrinkly, four hours later.

We still had some serious diving to do. Mike deGruy was going to attempt the deepest dive of the expedition with the help of a newt suit. This is a sort of one-man submersible; when Mike climbed into it, it made him look like a character from Toy Story. But this is no toy. It can take a diver to depths where the human body would be crushed to the size of a prune by the water pressure. Mike's mission was to go beyond the realm of the Fish Nerds and into the abyss.

In the meantime, I went to ride the Peleliu Express, one of Palau's best-known dive sites. We got into the water and finned over to the wall to drop down into the channel. The current was fierce, but once in the channel and going with it, we felt like we were flying; huge shoals of jacks drifted with us, and above and below us grey reef sharks cruised lazily past. But at some point we had to get out of the current and back to the top of the wall or we'd end up in the Philippines.

It is here that a Palau invention called a reef hook becomes necessary. The idea is to ascend to the top of the wall, hook on to the bare rock, hang in the current and watch the passing marine traffic. On this particular day the current was so strong we were rolled like tumbleweed towards the wall and it took everything I had to wedge my hook into position and not be carted away into oblivion. And I had no kit to carry.

Bob, a veteran underwater cameraman, swept past me upside down, before somehow managing to get a hold on the rock without losing his camera. I clung on for dear life, water battering against my mask and regulator, wondering why this was supposed to be fun. When I saw a young grey reef shark also being swept across the top of the wall, unable to swim against the ripping current, it was time to go.

More restful are the Blue Holes, where the Fish Nerds and I did our final dives. They descended to 140 metres with buckets and nets, looking like Victorian butterfly-hunters. I explored the spectacular topography of the shallows and the so-called Temple of Doom, a cave where turtle skeletons lie in the silt. During my second dive, I met Richard and the team decompressing at 40 metres. In the collection bucket was, among others, a beautiful fish: a new, previously unknown blue jewel from the deep. And, I realised as I admired it, I was one of the first people in the world to see it.

It is staggering that in 2008 there is still so much that we haven't discovered. In only a month we'd found more new species than anyone thought possible, and yet we'd barely scratched the surface. Chuuk, Yap and Palau may be truly on the diving map, but who knows how many secrets lie uncovered in those faraway waters of the Pacific?

'Pacific Abyss', a three-part series presented by Kate Humble, starts on BBC 1 tomorrow at 8pm

Traveller's Guide

Getting there

There are no direct flights between the UK and Micronesia, so you will have to get to Manila or Hong Kong and connect from there. Manila is served by Cathay Pacific (020-8834 8888; www.cathaypacific.com) via Hong Kong and Qatar Airways (0870 770 4215; www.qatarairways.com) via Doha. From Manila, Continental Micronesia (0845 607 6760; www.continental.com) flies to Guam and Palau; it also flies from Hong Kong to Guam.

To reduce the impact on the environment, you can buy an "offset" through Abta's Reduce my Footprint initiative (020-7637 2444; www.reducemyfootprint.travel).

Dive Worldwide (0845 130 6980; www.diveworldwide.com) offers trips to Micronesia. Prices for a 24-day tailor-made trip start at £3,125 per person, including flights 21 nights' B & B; and 10 dives. Permits are payable locally.

Diving there

Padi (0117 300 7234; www.padi.com) offers wreck diver speciality courses, which cover safety and conservation issues. The two-day courses start from £150. Those enrolling must already be certified as a Padi Advanced Open Water Diver.

More information

Federated States of Micronesia: 00 691 320 5133; www.visit-fsm.org

Palau Visitor's Authority: 00 680 488 2793; www.visit-palau.com