Biodiversity has become a central concept in agronomical research since the Rio de Janeiro summit in 1992. Agricultural areas include a unique biological diversity which is the basis of human activities. Conservation of this biodiversity in agricultural and protected areas is therefore fundamental and requires an operational approach. Biodiversity is a complex entity which can be spread over several levels (genes, species, ecosystems and ecological processes) and can be related to three main functions: (i) patrimonial functions, (ii) agronomical functions and (iii) ecological functions. The patrimonial function concerns conservation of the landscape aesthetic and threatened species. The biodiversity function according to relationships with agricultural activities describes resistance to biotic and abiotic stress, and the production of cultivated ecosystems. Biodiversity is also involved in ecological functioning through the existence of special habitats with particular species. The relevance of assessment tools is required in order to understand and evaluate the impact of farm practices on the different compartments of biodiversity on the patch scale to the landscape scale. Different methods, such as direct measurements with biodiversity indexes, biotic indicators and models are described and their suitability and limits are discussed.