Approaching Ternate from the air, the view is dominated by a green-sloped volcano rising from tropical blue sea. Look closer and you see small houses near the shoreline.

Ternate is an outpost of Indonesia, lying two time zones to the east of Jakarta, yet in local lore it's at the centre of the universe, having existed before the rest of the world came into being. When people in Hong Kong were engaged in little but farming and fishing, Ternate was a trade hub, visited by Chinese and Arab merchants drawn chiefly by the cloves grown here. It became the dominant power in the northern Moluccas, or Maluku, and from the 16th century was fought over by Portuguese, Dutch and Spanish forces for control of the Spice Islands.

To wildlife enthusiasts, Ternate has a special appeal - because, in 1858, British explorer-naturalist Alfred Russel Wallace added the island's name to an essay detailing his theory of evolution, which he formulated independently of Charles Darwin, who tends to get all of the plaudits. Wallace kept a house here for three years, using it as a base for journeys within the Moluccas and farther east, as he discovered a wealth of birds, butterflies and other animals, many of them new to science, and realised that this was a remarkable area of the world, where the plants and wildlife of Asia and Australasia merged. Today, the region is known as Wallacea.

Inspired by his book The Malay Archipelago, and enticed by the Spice Islands and the chance of adventure, I'm not exactly following in Wallace's footsteps - he roamed some 22,500km on more than 60 separate journeys! - but heading into the heart of Wallacea, with my wife and 10-year-old son, to seek out some of its unique species, including the naturalist's "greatest prize", the standardwing bird of paradise.

Our encounter with Wallacea wildlife begins on Sulawesi, which lies between the Moluccas and Borneo. As the world's 11th largest island - it is about 150 times larger than the territory of Hong Kong - Sulawesi has enough of natural and cultural interest to justify weeks of exploration but, sticking to a tight schedule, we head to the tip of the island's tendril-like, northeastern spur.

The lowland rainforest is protected within the Tangkoko National Park. Our guide, Irawan Halir, a local man who, with his thickset frame and shoulder-length hair, looks more like a rocker than a nature lover, leads us along paths and faint trails on gently sloping hills.

At times, there isn't a bird in sight but, with persistence, we encounter jungle treasures such as kingfishers, which are sometimes remarkably bold - one green-backed specimen, with rusty underparts, blue cap, green upperparts and brilliant red bill, is perched at eye-level and watches as I approach to take photos. Such birds are helping make Tangkoko a magnet for bird photographers.

A male red-knobbed hornbill, perhaps 80cm long from bill tip to tail tip, is much more imposing. He flies to a nest hole three or four storeys up a tree then regurgitates berry-sized figs before passing them through a tiny opening, to an unseen mate.

Irawan knows where spectral tarsiers rest during the daytime. They favour tangles of aerial roots supporting fig trees, emerging at dusk to prey on insects and small animals. Peering into one tangle, we find five tarsiers looking back at us, swivelling their heads as their huge eyes are too big to move in their sockets. Dwarfed by your average teddy bear, these are among the world's smallest primates - and the epitome of cute (although tarsiers, whose bodies average 12cm, were the inspiration behind Steven Spielberg's evil gremlins).

One day, a troop of black macaques stroll down to the trees fringing the beach looking statelier than Hong Kong macaques and deserving of the name "baboon-monkey", coined by Wallace. They, too, have made it into popular culture - a "monkey selfie" went viral last year, only for the owner of the camera to be challenged by a lawsuit claiming that the macaque should own the copyright to its self portrait.

"Bear cuscus - in that tree," says Irawan, as we walk up a slope. Through binoculars, we find three of these rather solemn-looking mammals resting in the crook of the tree. Bear cuscus are marsupials, belonging to the possum family that's common in Australia and thus serving as a reminder that this is Wallacea. Perhaps, like many of the other species unique to Sulawesi and nearby islands, their ancestors arrived on continental fragments that collided here, facilitating the complex geology and biodiversity.

This slender spur of Sulawesi is part of the rim of fire, and we drive some of the way up a volcano, then climb to the crater rim. It's dormant now, but we look across to a steaming crater on the slopes of Mount Lokon, which will erupt just 10 days after our visit, blasting volcanic ash up to 1,500 metres into the air.

Wallace passed here and stayed by an upland lake, where he remarked on the "general stagnation of bird and insect life". We stop for lunch beside a different lake, in the wooded crater of a dormant volcano, and find birds and insects abound, especially egrets and ducks.

By the shore, a sulphurous reek taints the air, steam billowing from bubbling pools of mud. While taking photos of the primeval scene, I am careful to keep some distance, mindful that, having visited mud springs in the area, Wallace told of a French gentleman who "ventured too near the liquid mud, when the crust gave way and he was engulfed in the horrible cauldron".

Although it's just a 35-minute flight across the Molucca Strait to Ternate, we find the Moluccas quite different to Sulawesi, and the world at large. Deep channels prevented many species from crossing the strait, even when the sea level fell during ice ages. Although the international traders are long gone, there are still transport links. Yet separation persists; even the internet proves a challenge to access on Ternate.

Maybe the sense of otherness is because the Moluccas were long divided into four sultanates. After the 48th sultan of Ternate, Mudaffar Sjah, was appointed to the position in 1975 it seems he became involved in political intrigues that led to strife between 1999 and 2002. Thousands of people were killed as conflict erupted, the warring parties including Christian and Muslim communities.

The people today seem relaxed and welcoming of outsiders. Visiting the sultan's palace, there's no sense of recent drama - instead, it's like a museum, with swords and suits of armour, ornate furniture, old photos and samples of the nutmeg, cloves and cinnamon that helped bring wealth to the Moluccas. We also learn that although the sultan died in February, his successor has yet to be chosen. While divine forces will guide the decision, I suspect mundane, political considerations will play their part, too.

Even in Wallace's day, Ternate was home to little wildlife of note. Although we see a vivid blue and orange kingfisher the size of a child's fist, we're heading for richer areas.

According to ethnobiologist Nasir Tamalene, who has joined us for part of the trip, Bacan is where Wallace discovered the standardwing. We travel to the island by ferry, which departs not at noon, as scheduled, but after Friday midday prayers. The ferry takes well over an hour to berth and both a hotel and restaurant prove hard to find.

Nevertheless, the next morning, as the day begins to break, I am led into the forest, using a torch to light the slender trail. I'm being guided by two men I met just minutes ago; one is maybe in his early 40s, the other perhaps 20. Neither speaks English; I'm limited to a handful of words of Indonesian. Not that there's time for conversation, for we're on a mission - to find Wallace's standardwing, one of only two birds of paradise found outside New Guinea and its islands.

On we go, up and over fallen logs, taking care not to brush thorny palm fronds, hearing the calls of exotic-sounding birds just out of sight. "Maleo," the older guide says, on hearing the loud whistle of a megapode, a game bird that builds mounds of leaves in which to lay its eggs, where they incubate in the warmth of rotting vegetation.

It's humid. I pause, sweating profusely, then move on again. The trail peters out and the guides use machetes to cut past shrubs, en route to a wooded slope where raucous birds call in the canopy. This is our destination: a standardwing lek.

As is typical in birds of paradise, male standardwings gather at display sites, called leks, where they show off their plumage in early-morning rituals, in the hope of impressing females enough for the chance to mate. The first standardwing Wallace saw had been shot by his assistant, Ali, who seemed much pleased with his efforts. Most of the body was ashy olive, with pale metallic violet on the head and side feathers that could be erected to form a pointed gorget. The unique features were two slender white feathers that sprang from the bend of each wing. These were about six inches long - the same as each wing, and, Wallace noted, they could be raised or laid along the body "at the pleasure of the bird": rather like ceremonial flags, or standards.

Standardwings are elusive. I can hear at least five but it takes time before I glimpse even one among the dense foliage.

A few days later, at another lek, I am treated to the full wonder of a display, and discover that the birds do indeed raise and lower their standards, as well as fly up from a perch before parachuting down on broad, pale grey wings before landing and dipping their heads until they are almost upside down. It's quite a routine, yet the one female I notice only briefly inspects the performance before disappearing.

Some other types of bird are more visible; a flock of parrots descends on a tree in search of fruit, the males scarlet but for their green wings - a dangerously beautiful combination that makes them popular in the bird trade, which is reducing wild populations.

Bacan's one small town, Labuha, is on the coast and consists only of low buildings, including brightly painted bungalows. Freshly caught tuna are arrayed on stalls in the wet market. Opposite, people are selling "Bacan stone", a blue-green, jade-like mineral that's popular in Indonesia, especially in the form of polished rounded gems affixed to chunky rings. Similar minerals are found locally, and two men proudly show off the rings adorning their fingers, one set with a white stone the size of a ping pong ball.

We stop for a look at the sultan of Bacan's house. It's far less grand than the palace on Ternate, a higgledy-piggledy white-washed building with sharply pointed green roofs.

"If you come back later, the sultan might see you," a guard says, to our surprise.

After sunset, we return, and sit in the reception room, surrounded by photos of sultans in ceremonial attire. I look in case there's a shot with Wallace, who met the then sultan 156 years ago, maybe on this very site, but there isn't. A tall, slender man enters, the sleeves of his striped shirt rolled up to the elbows.

The sultan, whose full name is Dede Muhammad Gary Ridwan Sjah, shakes our hands, diffidently remarking, "I hope you're not too disappointed." On the contrary, we're relieved by the lack of formality, and relate a little of our travels. The sultan agrees with my suggestion the island might benefit from ecotourism, but he doesn't want Bacan to host a brash resort.

Ecotourism is hardly a novel idea in these parts. It was mentioned in a plan for the Aketajawe-Lolobata National Park, established on nearby Halmahera - the largest of the Moluccas - in 2004. But when we visit the park, there's scant evidence the suggestion has been followed up on.

There is, however, much that could appeal to anyone with a love of wildlife and wild places. Tamalene takes us to a hamlet of wooden houses on stilts, where he finds two men to guide us into the jungle. We follow a river upstream, several times wading across thigh-deep channels, discovering the kind of pristine forest that has almost disappeared from places such as Borneo.

Forest people live here, hunting with bows and arrows. Our guides have married into the forest tribe; one says he did so after his now father-in-law threatened to kill him should he refuse his daughter's hand in marriage.

Although Wallace barely explored this island, he knew from his collectors and other sources that it was rich in birdlife more Australian than Asian in character. It was perhaps while staying here, recovering from a fever, that he hit upon his theory of evolution.

Wallace wrote the essay "On the Tendency of Species to Form Varieties; and On the Perpetuation of Varieties and Species by Natural Means of Selection", marking the work with the word "Ternate", from where it was posted to Darwin. The more famous scientist would write to a mutual friend, "If Wallace had my manuscript sketch written out in 1842, he could not have made a better short extract!" (In 1842, Darwin wrote his first pencil sketch of his theory of natural selection; his landmark On the Origin of Species would not be published until 1859.)

One of the Moluccas' most common birds is especially interesting. It's a kind of flycatcher but, unlike similar birds elsewhere, these creatures - willie wagtails - are as bold as brass, perching atop bushes, sometimes flying over houses. They remind me of the common bulbuls in places such as Hong Kong but there are no bulbuls here and the willie wagtails seem to have readily taken their niche.

I see two willie wagtails foraging for insects in Pak Roji's garden, just inside the national park boundary. Properly known as Mahroji Akejawe, Roji is a farmer with a passion for the jungle and its wildlife. Slender, with a ready smile, he doesn't seem tough to look at, yet he'll hike for three days to a coastal market to buy cattle on behalf of his neighbours.

During a stint as a porter for bird-survey teams, he developed an interest in birdwatching.

Roji takes us on a jungle foray, during which we have splendid views of standardwings and pause to admire an immense tree - its buttress roots perhaps as wide as a couple of buses. Venturing into a small cave, we disturb a few roosting bats and take care not to crack heads on stalactites as we scramble down to a still, clear pool.

"There's a nearby cave that a French team explored for a week, but they ran out of time before reaching the end," says Roji.

There's no need to head deep into the forest to find birds. From the veranda of Roji's wooden farmhouse we watch colourful kingfishers and bee-eaters. A stream just behind the house is sometimes the world's best place to see the flightless invisible rail - although for me it lives up to its name.

I'm far luckier with another speciality, which Wallace rated "one of the most beautiful birds of the East": the ivory-breasted pitta. Pittas are thrush-like ground-feeding birds, renowned among birdwatchers for being hard to see even though they can be as colourful as kingfishers. Roji has built a screen of banana leaves by an area a pitta likes to feed in and, on our last afternoon, I sit behind it, camera at the ready.

A pitta hops into view. It stands upright and, at first glance, looks black above, white below. But I also notice a red patch on its belly, and shining green on its wings. It's exquisite. The pitta seems curious about the lens protruding through the leaves and hops closer, coming so near I feel I could almost reach out and touch it. Then, it moves off, and melts away into the forest.

It's time for me to go, too; the next morning we fly to Jakarta.

As I stand, I have a huge smile on my face, partly because I know few birdwatchers have seen and fewer still photographed this magnificent pitta, one of the wild wonders of Wallacea.