Let’s get this straight: you won’t see lions, zebras, giraffes or hippos. You will see human beings. And though the jungles and beaches might fall short of computer-generated perfection, they are far more exciting than anything you’ve seen on screen. The DreamWorks animation may have been a free advert for a country that sees criminally few visitors, but while they’re trading on the exoticism of its name, you’ve got to wonder – why not just stick to the truth?

Skipping back a mere 165 million years, Madagascar was at the heart of Gondwana, where new species of plants, mammals and birds were beginning to flourish among the dinosaurs. When what is now the world’s fourth largest island drifted off from the African mainland, it took with it prime stock, whose descendants are still there. Over the next 100 million years or so, extras continued to rock up and make it their home. The present-day result is more unique weirdness than big game – but compared to this, The Lion King is so five minutes ago.

Which is why the first night of our honeymoon found my husband and I on rickety campbeds in the middle of the rainforest, listening for something that looks like an overstuffed teddy bear and sounds like a fire engine. Soa Camp at Anjozorobe, an hour’s drive from the capital Antananarivo, is a small-scale example of how the country is waking up to the opportunities of eco-tourism. A night walk had whet our appetites with Parson’s chameleons, tree frogs and leaf-tailed geckos but the teddy-like indri remained elusive.

The indri is the largest example of the reason most people come here: lemurs. A primate order found nowhere else on Earth, these delightful, lanky-limbed creatures were replaced by an updated model – the monkey – everywhere else, but thanks to some stowaways, some 51 varieties exist in Madagascar.

Our first lemur sighting was no disappointment. Having flown to the 400,000ha private reserve of Anjajavy in the remote north-west, they were virtually there to welcome us: a troop of white furry bodies in the treetops, black faces gazing down at us with interest. Coquerel’s sifaka, we soon learned – another family of which had taken up residence outside our bungalow. Between these, the resident chameleons and the antics of the brown lemurs visiting the gardens at tea-time, tearing ourselves away to go sun-bathing was surprisingly difficult.

In a country where 80% of the flora and fauna are endemic – a fact you’ll find yourself repeating endlessly in an attempt to explain to others just how incredible the place is – lemurs are really just the tip of the biodiversity iceberg. The widely differing habitats that exist on the island range from subtropical rainforest and undulating grassland to spikily surreal labyrinths of tsingy, a hard limestone rock that takes its name from a local word meaning ‘to walk on tiptoe’ (graze your knee on the stuff and you’ll know why).

It was down in the arid south that we realised why, like the tsingy, Madagascar’s plant-life is just too odd not to commit to film. Just a few minutes’ walk from the village of Ifaty and we were into the remarkable ‘spiny forest’, a psychedelic landscape of orange sand sprouting wayward-tentacled octopus trees, bulbous elephant foot plants, multicoloured aloes and the majestic baobabs for which it is most famed. With bloated trunks and stunted branches, they’re like trees wrenched from the ground and stuck back in upside down – yet here, they look positively normal. This is landscape gardening on acid.

Even without the weirdness, the significance of what’s around you is considerable – and increasingly, efforts are being made to ensure that visitors know this. Not being much of a twitcher, the ultra-rare Benson’s Rock Thrush hadn’t really ever figured on my radar before being told I was looking at one. Yet gazing at this delicate grey and orange bird, I suddenly felt blessed. Madagascar makes an eco-tourist of you whether you like it or not.

However, pointing out the importance of this natural bounty to visitors is one thing; convincing the locals of it is another. Slash and burn farming practices have permanently destroyed large swathes of rainforest, yet poverty-stricken Malagasy farmers have little choice but to continue in order to feed their families. Increasingly Madagascar’s ecosystems also face threat from another of the country’s natural resources: sapphires.

Driving between Isalo National Park and the large southern town of Tulear took us through the heart of Madagascar’s gem boom. Now a seething hub of shops, traffic and people, Ilakaka didn’t even exist a decade ago. Almost a tourist attraction in themselves, these ‘sapphire towns’ that have sprung up along the main road from Tulear are the closest you’ll come to a jeep safari – one look at the dubious gem shacks and heavily-armed flunkeys and you’ll understand your guide’s advice to stay in the car.

The true threat isn’t quite so visible. Inaugurated in 2002, Zombitse-Vohibasia National Park is one of the last remaining areas of transition forest in an area devastated by deforestation. It is one of the few places where ring-tails and brown lemurs co-exist; it’s also the only place in the world to see Appert’s greenbul, one of Madagascar’s rarest endemic bird species. It also however sits on top of potential millions in sapphires, and though mining within the park is outlawed, our local guide hints that bribe-friendly officials ensure it still happens.

Madagascar’s treasures are myriad, but their future is fragile. If more species are to avoid the fate of the now-extinct elephant bird, then environmental protection must become a way of life, not just a means of drawing in eco-tourists.

At Zombitse, it is the local people who have been the project’s strength. Environmental groups have worked closely with the Bara community, for whom the forest is an integral part of their social and economic traditions, the tribal patriarchs acting as guardians for it. Their story may not seem quite as exciting as the adventures of some shipwrecked zoo animals, but this is the kind of one we need to pay attention to.