This special issue contains an editorial and 6 papers discussing various topics on agroforestry and biodiversity conservation, including: dung beetle and terrestrial mammal diversity in forests, indigenous agroforestry systems and plantain monocultures in Talamanca, Costa Rica; bat and bird assemblages from forests and shade cacao plantations in two contrasting landscapes in the Atlantic forest of southern Bahia, Brazil; tree biodiversity, land dynamics and farmers' strategies on the agricultural frontier of southwestern Burkina Faso; linking trees on farms with biodiversity conservation in subsistence farming systems in Nepal; indigenous knowledge and management of Araucaria araucana forest in the Chilean Andes: implications for native forest conservation; and the policy terrain in protected area landscapes: challenges for agroforestry in integrated landscape conservation.