The dhow is like a time capsule. Sails flap and crack overhead; woven palm-leaf panels, lashed to the sides of the vessel with hand-made coconut-fibre rope, offer protection from sea spray. The timbers creak and sigh like old gossips. If it wasn't for 10-odd brightly clad tourists with various degrees of sunburn and an incongruous outboard motor, we could have been some 500 years back in time, when Arab traders still controlled the coasts and channels of Mozambique's Quirimbas Archipelago.

Back then, the cargo was turtle shell, ivory, amber and woebegone slaves. All we're after is a golden crescent of sand that emerges phoenix-like from the waves as the tide recedes. It's prosaically known as the Sandbank, and it's one of Ibo Island Lodge's many treats. When tides permit, lodge guests clamber aboard a dhow and head for this immaculate patch of private beach that appears mid-ocean, some 45 minutes away.

Once deposited on the sun-kissed curl, everyone takes to the water to eyeball the marine life that frolics around pristine coral "bommies": from Picasso triggerfish and spotted sweetlips to the bonkers attire of squirrelfish. When we finally surface, it's to find that lodge chefs Joshua and Mary-Ann (who'd sailed ahead on another boat with supplies), had brewed coffee and beaten eggs: breakfast is served on a sweep of linen-clad tables and chairs on the sand. Then we bake and swim until the tide eats up the sand once more.

This superlative moment is one of many in a visit to Ibo, one of 32 islands in the neon-blue waters of the archipelago, and one of 11 that make up the Quirimbas National Park. Covered in a shaggy coat of tropical vegetation, Ibo has considerable natural beauty, but it is not a simple beach destination. Instead, it is surrounded by reefs and groves of mangroves - the park has one of the largest mangrove forests in Africa - and its charm resides in village life and a rich cache of ancient stories.

Ibo, set to attain World Heritage Site status soon, has a total of three cars and a ramshackle shoal of motorcycles. It also has a smattering of generators (no grid electricity). The past is reflected in the decaying villas and crumbling architecture of the Old Town - all flamboyant trees, sandy streets and kids playing old-fashioned games like spinning tyres. Arab, Indian and Chinese influences abound (there are graves that bear ancient Chinese script). It breathes history. Much is said about the 1500s and 1600s, when Arabs initiated the slave trade and the Portuguese enthusiastically took over. But the recent past is as dramatic.

In the shadows of a veranda, João Baptiste, a local historian getting on in years, waves us over for a quick lesson. Frelimo (the liberation party that has ruled Mozambique since independence) posters adorn the walls of his home. Our Portuguese is rusty, but we get the basics. Baptiste is known here as the first black child to be admitted to the local school; he later worked as an administrative clerk. He speaks of the war; of a book he is working on, and of independence. "The Portuguese were bad, so bad," he says.

The evening before, we'd wandered the town on an historical tour with a guide named Ali. The standout landmark is the Fort of São João Batista (1791); a pentagonal building with a sun-drenched courtyard and some seriously eerie rooms. (Our tour also took us to two more forts, one dotted with goat droppings, the other slowly being restored.) Slaves were held in São João Batista before being shipped off; more recently, Frelimo supporters were jailed, tortured and killed here in the years before independence in 1975. Hundreds are said to have been buried in the sand underneath the coconut palms.

Nowadays, the fort is full of silversmiths. All day long they turn old Portuguese coins into gossamer threads of metal; then fashion the silver into jewellery in a poignant ode to beauty.

The turbulent past is responsible for Ibo's ghostly air. Post-independence, the Portuguese were ordered to leave within days; later many of the abandoned villas and mansions were plundered. Some are ruins; shells topped with the odd strangler fig. Money to buy and restore the old buildings, some dating back to the 1700s, is scarce. Most Ibo locals - there are about 4000 on the island - still live outside the Old Town, contributing to its spooky, forgotten charm. As do wisps of stories - like the wife who decorated the facade of her home with cowry shells, one for every time her husband travelled abroad; or another devoted wife who refused to believe her dead husband had truly departed: for years she placed food alongside his coffin, which was inevitably consumed by needy villagers.

There is much to do on Ibo, and much of it is aided by Ibo Island Lodge. The hosts tempt you out of its beautiful rooms and spider-lily-infested gardens with treats like sunset cruises, bird walks, kayaking among the mangroves, diving and (for those with deep pockets and plenty of time) tailor-made trips to private islands. (Full dhow and canoe safaris are also an option.) By sunset, replete guests trickle back for drinks on a balcony overlooking the mangroves. We sleepily sip beer, dine in the warm dusk, and listen as a guide named Cosmo points out the constellations wheeling above us. General manager Rob McKenzie tells us to listen for distant rhythmic beats at night: humpback dolphins slam their tails on the water's surface in a sophisticated group hunting method.

Of course, there are times when the less there is on an island, the better. Just north of Ibo is Matemo, where an arc of palm-thatched chalets decorate a sandy shore. This Rani Resort property is pure indulgence: just right for honeymooners, families and others seeking time out and extreme cosseting - this time with a beach. We arrived with two young Italian honeymooners, whose suitcases had somehow been left behind in another African city (yup, blame OR Tambo). Within hours, they were scampering along the beach scantily clad, the loss forgotten: Matemo is not the kind of place where one worries about dressing up - or about anything much at all. The only creatures dragging around baggage are the countless hermit crabs (just about every roomy exotic shell walks away unexpectedly as you approach).

Matemo's pleasures revolve around sun and sea. We floated off a reef in teeming clouds of fish, like vivid, live confetti. On land, we admired gigantic island baobabs and spent a glorious evening cycling up and down the airstrip, in search of pipits and other birds. I bet many feel no urge to leave the beach, but it's possible to go further than the resort's borders. It was on a tour of some of Matemo's seven villages, where homes are built with blocks of coral, that it struck home quite how remote the Quirimbas are.

In the villages, soccer is hugely popular and local teams vie for the Aujan Cup - named after Rani founder Adel Aujan (he has built both schools and mosques on the island).

But otherwise, most people live as they always have: fishing and bartering; growing cassava and gathering local fruit. Villagers stared at us, fascinated. One lovely young woman had painted her face white with pounded bark from a local tree, a beauty treatment favoured by those about to get married and an effective sunscreen. After due congratulations on her engagement had been exchanged, she fixed the honeymooners with a candid stare and asked what the drawing was on the man's skin. She'd never seen a tattoo. "It's decoration, like your face paint, or earrings," the Italians explained.

The woman laughed. "I think I prefer earrings."

• Stephen was a guest of Rani Resorts and Ibo Island Lodge