The Mediterranean basin is one of the most important biodiversity hotspots. However, only 5% of its original vegetation is still in place, and the landscape has been managed and transformed by humans for at least the last two millennia. In the last century the mechanization of agriculture and the overuse of semi-natural habitats have influenced the region even more than before, with huge consequences, especially on islands. Sardinia is the second largest island in the Mediterranean basin, and it has been considered for long as a semi-natural area with an economy based on traditional agroforestry and pastoral practices. Considering four maps covering Sardinia and ranging from 1935 to 2007, we measured the rate of forest changes demonstrating a constant trend towards forest increase, and with a complete recovery of the total forest surface compared to the late 1800s.The traditional agroforestry practices decrease in time due to socio-economic reasons, with deeper consequences for the mosaic of traditional agricultural areas and semi-natural habitats, as well as for the conservation of the unique biodiversity of Sardinia. Species typically linked to Mediterranean forests recovered and are recovering, while species linked to traditional semi-natural landscapes decreased, facing conservation problems. We suggest that the current challenges for biodiversity conservation in the island should be focused together with the agricultural policies towards the preservation and improvement of traditional open areas, even important in the history of the entire Mediterranean hotspot.