When travellers dream of African islands, the names that usually surface are familiar: Zanzibar, Mauritius, the Seychelles. But beyond the glossy brochures lie chains of islands few have heard of, where dhow sails catch the same winds as 16th-century spice traders and volcanic cliffs tumble into reefs teeming with marine life.
Medjumbe Island Pool Deck/Ewald De Korte/Wikimedia Commons
From the remote Quirimbas Archipelago in Mozambique to the emerald twin isles of São Tomé & Príncipe and the Comoros, these are Africa’s hidden archipelagos. To explore them properly, you don’t just fly in and flop on a beach chair. You set sail.
Mozambique’s Quirimbas: Sailing with history
Ibo Island/Rosino/Wikimedia Commons
Stretching along northern Mozambique’s turquoise coastline, the Quirimbas Archipelago is a string of more than 30 coral islands scattered across 400km of the Indian Ocean. Unlike its more famous neighbour, Zanzibar, the Quirimbas feels like a world suspended in time.
At the heart of the chain is Ibo Island, once a bustling Portuguese trading post. Today, crumbling colonial mansions and ancient forts tell stories of merchants, missionaries, and explorers. Walking through its streets, you hear Swahili, Portuguese, and Makua spoken in a rhythm unchanged for centuries.
But the real magic begins when you push off in a traditional dhow. Many operators run multi-day dhow safaris, where travellers sleep on deck under the stars or set up camp on deserted sandbanks. Days are spent paddling through mangrove forests, snorkelling untouched reefs, or spotting dugongs grazing on seagrass beds.
Luxury doesn’t go amiss either. Islands like Quilalea and Medjumbe offer eco-lodges where sustainability meets barefoot indulgence — think solar-powered villas and candlelit dinners on the beach.
Getting there: Access via Pemba (direct flights from Johannesburg or Dar es Salaam). From there, charters and dhow safaris whisk you into the archipelago.
ALSO READ: Spice, storytelling, and souks: The cultural trails of Zanzibar & Lamu
São Tomé & Príncipe: Cocoa, craters and coastlines
Ilhéu das Rolas/Ji-Elle/Wikimedia Commons
Fly six hours west across the continent and you’ll find Africa’s tropical heartbeats — São Tomé & Príncipe. This two-island nation, the second-smallest country in Africa, is often called the “Galápagos of Africa” for its biodiversity and volcanic landscapes.
Príncipe, a UNESCO Biosphere Reserve, feels like a film set: emerald rainforest spilling into empty black-sand coves, volcanic plugs rising like spires, and humpback whales breaching offshore. Inland, abandoned Portuguese plantations, or roças, are being transformed into guesthouses, where you can sip coffee grown on the very slopes you’ve hiked.
Chocolate lovers won’t want to miss São Tomé. Once the world’s largest cocoa producer, the island is still dotted with cacao groves where visitors can trace the journey from bean to bar — and taste some of the purest chocolate on the planet.
Sailing here means hopping between hidden bays and palm-fringed beaches, spotting rare birds like the São Tomé green pigeon, or anchoring near the Ilhéu das Rolas, which sits exactly on the Equator.
Getting there: Flights connect via Lisbon, Accra, or Luanda. Yachts and catamarans can be chartered locally for island-hopping.
The Comoros: Volcanic isles of fire and spice
Sandy beach north of Mitsamiouli, Grande Comore, Comoros/Radosław Botev/Wikimedia Commons
Where the Indian Ocean brushes up against the northern tip of Madagascar lies an archipelago that travellers often overlook: the Comoros. With their mix of Swahili, Arab, Malagasy, and French influences, the islands feel like a cultural tapestry woven across centuries of seafaring.
Moroni, the capital, smells of ylang-ylang and cloves — the country is one of the world’s top producers of essential oils. It’s Medina, with narrow alleys and carved doors, hints at Zanzibar but without the crowds.
Adventure seekers will find plenty offshore. The Comorian waters are a sanctuary for humpback whales, which migrate here between July and October. Divers can encounter manta rays, dolphins, and an impressive array of reef fish. And looming over it all is Mount Karthala, one of the world’s largest active volcanoes, where hardy trekkers can peer into a mile-wide crater.
Sailing between the islands is a way to experience the Comoros at its most authentic: quiet beaches with no footprints, fishing villages where hospitality is as natural as the tides, and sunsets that seem to last longer here.
Getting there: The Comoros are accessible via flights from Nairobi, Dar es Salaam, and Mayotte. Local ferries and chartered boats are the best way to island-hop.
Why these islands matter now
Beyond their beauty, these hidden archipelagos represent something rare: a chance to experience African islands without the heavy footprint of mass tourism. They offer sustainable travel opportunities where communities benefit directly, whether through eco-lodges in Mozambique, cocoa cooperatives in São Tomé, or spice farming in the Comoros.
For travellers seeking something different — the romance of sailing, the thrill of discovery, and the chance to explore cultures shaped by centuries of ocean trade — these islands are the future of meaningful island travel.
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