He also pleaded for the government to fight the corruption that is ravaging the island's environment and keeping its people in "inhumane poverty".
Francis urged President Andry Rajoelina to provide Madagascar's people with jobs and alternative sources of income so they aren't forced to cut down trees to find fertile soil, poach the island's wildlife and engage in contraband and illegal exportation of its diverse flora, fauna and mineral resources.
"The deterioration of that biodiversity compromises the future of the country and of the earth, our common home," Francis warned Mr Rajoelina and other government authorities as he began the second leg of his week-long trip to southern Africa.
Madagascar is home to 5% of the world's plant and animal species, with around 95% of its reptiles and 89% of its plant life existing nowhere else on Earth, according to the World Wildlife Fund.
Yet it is also one of the world's poorest countries, with 75% of its 25.5 million people living on less than two US dollars a day.
Environmental groups and Transparency International have long highlighted the illegal logging of Madagascar's rosewood forests and other endangered tree species as evidence of the rampant corruption that has made multimillionaires out of a few "rosewood barons" who have plundered the island's northeastern forests.
"Your lovely island of Madagascar is rich in plant and animal biodiversity, yet this treasure is especially threatened by excessive deforestation, from which some profit," Francis said.
He cited forest fires, poaching and the "unrestricted cutting down of valuable woodlands" as particular threats.
More so than any pope before him, Francis has made environmental concerns a pillar of his papacy, linking global warming to the persistent exploitation of the world's poor by the wealthy.
He has issued an entire encyclical on the need to care for God's creation and next month will preside over a meeting of bishops from the Amazon, where an outbreak of rainforest fires have once again focused international attention on the need to preserve what he calls the "lungs of the planet".
Francis has also frequently called attention to the devastation wrought on the poor by corruption, often calling public officials to account on his foreign trips.
Transparency International, which ranks Madagascar among the most corrupt countries, has accused local public officials of complicity or negligence in the illegal logging, mining of gold and sapphires and the poaching of tortoises, turtles and exportation of lemurs.
In his speech, Francis urged Mr Rajoelina, who came to power on a campaign to fight corruption, to make good on his pledges.
"I would encourage you to fight with strength and determination against all endemic forms of corruption and speculation that increase social disparity, and to confront the situations of great instability and exclusion that always create conditions of inhumane poverty," he said.
Francis, the world's first pope from the global south, acknowledged that some of the island's poor have no choice but to cut down forests to find soil or extract minerals in illegal ways that damage the environment.
"So it is important to create jobs and activities that generate income, while protecting the environment and helping people to emerge from poverty," he said.
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