A large lizard sits sunning itself on the rugged volcanic rock. A moment later an identical reptile appears alongside it, glistening in the midday heat. Within minutes the grey-brown, earthy tones of the coastline have been turned a shimmering black as dozens of marine iguanas leap out of the choppy sea to warm themselves after a dip in the chilly Pacific.

Our guide points to a sea turtle, whose head occasionally breaks the surface before heading down into the blue depths in search of the lush green algae that the iguanas also love to eat. Away in the distance a colony of sea lions frolics offshore while bright red rock crabs scuttle among the nooks and crannies of the coast.

This image was probably one of the first the Bishop of Panamá Fray Tomás de Berlanga saw when his ship was blown off course and bumped into the then undiscovered Galapagos Islands in 1535, thus becoming the first European to set eyes on the huge, varied array of distinct flora and fauna that lived there.

When Charles Darwin arrived on the islands some 300 years later this flourishing sea scene brought on revulsion.

“The black lava rocks on the beach are frequented by large, disgusting clumsy lizards. They are as black as the porous rocks over which they crawl and seek their prey from the sea. I call them ‘imps of darkness’. They assuredly well become the land they inhabit,” Darwin wrote.

While the naturalist may not have been the biggest fan of the iguanas, they, alongside 14 other species known collectively as the ‘big 15’ are today the Galapagos’ greatest attraction.

His modest, 19-island archipelago some 600 miles west of Ecuador is now a Unesco World Heritage Site, a biosphere reserve, the world’s second largest marine reserve and one of the few examples of successfully limiting human encroachment into environmentally sensitive areas.

It’s the jewel in Ecuador’s crown. But there’s more to the country that derives its name from the equator that runs almost straight through it. This small South American state sandwiched between Colombia to the north and Peru to the east and south has been declared by many experts to have more biodiversity than anywhere else on earth. And I was determined to sample some of it.

A forest in the clouds

Most international flights bring travellers into Quito, the country’s capital and the first place – alongside Krakow in Poland – to be declared an official World Heritage Site by Unesco in 1978.

Squashed between three active snow-capped volcanoes, the city is perched on and around a plateau some 10,000ft above sea level, making it the world’s highest capital city. It sprawls high into the surrounding hills, but the focal point for many is the historic centre.

It was here Spanish conquistadors set up the administrative heart of their Latin empire, and it’s the location of my first stop. Looking over the Plaza de San Francisco and the monastery of the same name, is the Casa Gangotena hotel.

Situated inside a renovated historic mansion that was previously home to several of Ecuador’s presidents, it’s an exquisitely decorated 31-room hotel filled with roses and orchids. There’s a roof terrace offering views of the city as it sprawls down the valley out to the west.

The old city itself is the largest collection of intact colonial buildings in the Americas, with some 5,000 properties designated historically significant. Among those are churches. A lot of them.

Three hours away, in the foothills of the Andes, there’s a cloud forest that holds more species of orchid, butterfly and bird than all of Europe combined.

Inside the monastery on San Francisco Plaza, you’d be forgiven for thinking that the place of worship for dozens of monks would be a pretty modest affair. But the church of San Francisco was built at a time when Spanish architecture was about projections of power and wealth.

The original tower was for hundreds of years the tallest structure in the city before an earthquake brought it crashing down. It has since been rebuilt at a safer height. Inside, the ceilings are covered in intricate hand-carved awnings while the walls are adorned in gold leaf.

It’s a theme you’ll find in nearly all of the old city’s religious buildings. La Iglesia de la Compañía de Jesús, known colloquially as La Compañía, is a Jesuit church little more than 100m away that has gold leaf plastered across the giant double doors for passers-by to see.

Spanish soldiers in the 16th century quickly discovered vast quantities of gold and silver under Incan control, and the churches of Quito were to be the displays of their spoils. But while the old colonial capital was fascinating, I was here to discover the jewels of the natural world.

Just three hours away by bus, in the foothills of the Andes, there’s a cloud forest – a type of rainforest – that holds more species of orchid, butterfly and bird than all of Europe combined.

Ecuador’s cloud forests are part of a larger stretch of woodland called the Tumbes-Chocó-Magdalena, or El Choco to locals. This hotspot of biodiversity reaches from Panama in the north down to Peru in the south. However, most of the forest in those countries has been logged or removed in favour of pasture for cattle.

The perimeter of the hotel is patrolled by guards and makes you feel like you’re entering Jurassic Park with its giant wooden gates.

However, the area surrounding Mashpi Lodge – my home for three days – is surrounded by what scientists call ‘primary forest’. This an area that has had zero contact with people – and as such, retains its incredible levels of biodiversity.

Getting to the lodge requires traversing a rocky dirt track, originally created as a logging road to gain access to the deeper parts of the forest but since abandoned. The perimeter of the hotel is patrolled by guards and makes you feel like you’re entering Jurassic Park with its giant wooden gates.

However, upon arriving at the hotel, you’re taken aback by the clean, minimal lines and huge panes of glass nestled in the dense green of the cloud forest.

I was greeted with a juice made from fruit picked locally that day and a cooling towel before being shown my room. Each suite has floor-to-ceiling glass facing out into the jungle. “It’s the best widescreen TV money can buy,” the porter tells me.

Everything about the hotel is geared towards the outdoors. There are two viewing platforms on the roof allowing visitors to gaze across the verdant views occasionally spotting toucans, and hear the low wails of howling monkeys feeding on fresh leaves in the canopy.

Within four hours of leaving the capital, we were trekking through dense forests. And when I say dense, I mean dense: cloud forests are unique thanks to the fact their near constant temperatures and rainfall – almost double what you’d find in the Amazon mean the ecosystem has dozens of epiphytes, or plants that live on each other.

There are mosses on the trunks of trees, orchids between the mosses, ferns growing on branches, algae covering leaves. If it’s green, there’s something growing on it. Which makes seeing wildlife incredibly tricky, were it not for our guides.

They can spot glass frogs – amphibians with translucent skin – sitting on giant leaves, locals call elephant’s ears, tiny camouflaged snakes known as colubrids slithering through the undergrowth and giant umbrella birds perched on distant branches with absolute ease.

But perhaps the biggest draw of the Mashpi Lodge is its humming bird station. At dawn the next day we drove up to a series of benches that appeared to be placed at random. But as we got closer, we could see tiny birds darting around.

Over three short days I got to swim in hidden waterfalls, see more wildlife than I ever thought possible outside of a zoo.

The reserve has 22 species of hummingbird, all featuring distinct colours, sizes and adaptations to the tiny ecosystems they reside in. Thanks to a few strategically placed bananas and nectar pots, they flock to the station to feed every morning. It was an unforgettable experience.

Over three short days I got to swim in hidden waterfalls, see more wildlife than I ever thought possible outside of a zoo and ride a bicycle across the forest canopy via the hotel’s skybike – a crude steel tube frame, a few peddles and a cable stretching out over a vast ravine below. It’s an amazing way to experience this corner of the world.

But at the risk of forgetting why I came to Ecuador, I returned to Quito for a four-hour flight to Baltra island on the Galapagos.

Islands born out of the ashes

I arrived on the archipelago in the cool, dry season. But thanks to its position straddling the equator, Galapagos in winter has a balmy average temperature of 24°C.

I was here to see the islands, but before boarding the expedition ship Santa Cruz II, I was in need of some well-needed R&R after the days spent trekking through the primary forests of El Choco.

I checked into the Finch Bay Eco Hotel, a boutique destination designated the world’s leading green hotel two years running. Set just back from the beach, this quiet, discreet hotel is tucked away from the town of Puerto Ayora and accessible via water taxi. Here, you’ll share a bench with sleeping sea lions and red rock crabs.

The hotel has its own private yacht allowing you to explore the huge swathes of nearby islands including Santa Fe, North Seymour and South Plaza. All boast iguanas, seals, sea lions and boobies both of the blue and red-footed varieties. But I wanted to explore the more emote parts of the Galapagos, where whale sharks drift in the ocean currents and where Darwin’s finches feed alongside the flamingos. Yes, flamingos. I was definitely going to need a bigger boat.

The Santa Cruz II is a recently commissioned luxury expedition ship, capable of carrying 90 guests in opulence into the lesser-known reaches of the islands. Departing from Baltra Bay, our first stop was Las Bachas beach and its briny lagoons. Named after the barges the US military left there at the end of the second world war, today flamingos wade through the warm pools of water sat behind the beach.

We watched the sun set behind the International Date Line a few thousand miles away to the west before eating a sumptuous dinner on board.

The next morning we set off for a quick sail over to Santiago island and Buccaneer Cove. Named thanks to its reputation as a temporary home for British pirates who were looking to surprise Spanish merchant ships leaving mainland South America full of gold, today its inhabitants are made up of nesting birds including petrels, shearwaters, nazca boobies and their non-flying cousins, the Galapagos penguin. Beneath us were dozens of Galapagos sharks, parrot fish and bright, orange-speckled starfish. I’d never seen such high concentrations of wildlife.

As a country that’s roughly the same size of the UK, with the history of Peru, bio-diversity of Brazil and the transport links of a western European country, Ecuador really has so much to explore.

From there it was a short zodiac ride to Puerto Egas, a long, flat, black lava shoreline where eroded shapes form lava pools, caves and inlets that offer shelter for birds, fish and sea lion pups.

The area is named after Dario Egas, the owner of a salt mine on the island, who at one point was the only salt producer in all of Ecuador. The mining has gone elsewhere, but you can still see the scars of the excavations among the scrub.

Off in the distance Santiago loomed, but the best view of the island was in fact on the tiny Bartolome island to Santiago’s east. Created by volcanoes, the landscape is dominated by the cinder cones that brought magma from the earth’s core to create a lunar-like terrain that still bears the scars of past eruptions. Most of Santiago’s size is attributed to low, jagged lava flows that stretch into the Pacific.

Watching over proceedings is Pinnacle Rock, a jagged, shark-tooth shape rock structure that came into being after the US Navy used the formation as target practice during the second world war.

From those incredible views over the islands, it was back to the boat for an overnight sail to San Cristobal island, where the cruise came to an end.

As a country that’s roughly the same size of the UK, with the history of Peru, bio-diversity of Brazil and the transport links of a western European country, Ecuador really has so much to explore.

Jacada Travel (jacadatravel.com; 020 31 314 586) offers ten-night trips to Ecuador and the Galapagos, including a Galapagos cruise and stays at Casa Gangotena, Mashpi Lodge and the Finch Bay Eco Hotel from £7,113pp, including flights.