Ecosystems are the basis of life and all human activities. Agroecology as an approach to foster the transition to food systems that conserve resources and improve human well-being, has been increasingly promoted by scientists, Non-Governmental Organization (NGOs), international organizations, and peasant movements. Conservation of biological diversity is very important for the proper functioning of the ecosystem and for delivering ecosystem services. Maintaining high biodiversity in agroecosystems makes agricultural production more sustainable and economically viable. During the last decades, worldwide losses of biodiversity have occurred at an unprecedented scale and agricultural intensification has been a major driver of this global change. Comprised into 14 chapters, this book integrates state of the art trends and challenges on biodiversity in agricultural ecosystems at both local and global perspective. This book opens with a chapter on plant diversity in agroecosystems and agricultural landscapes. Agricultural landscapes represent a cultural landscape group. Their origin, structure and ecological relations differ from natural landscapes considerably. Agroecology is increasingly promoted by scientists, non-governmental organizations (NGO’s), international organizations and peasant movements as an approach to foster the transition to sustainable and equitable food systems. The challenges to agroecological transitions are not the same for all farmers, as they can face different social and bio-physical conditions. This book, next, intends to assess how agroecological practices and principles are associated with different farm types within a process of agroecological transition. It assesses variations between farm types and describes implications for promoting transitions. It also discusses how and why quantitative and participatory methodologies can be combined for more precise and relevant assessments to understand and promote agroecological transitions. The protection of ecosystems and biodiversity is an important task and a key challenge to the world. Therefore, the next chapter focuses on the role of biological diversity in agroecosystems and organic farming. Further, this book takes a look on the governance of ecosystem services in agroecology; the ecology of plant chemistry and multi-species interactions in diversified agroecosystems; activity and variety of soil microorganisms depending on the diversity of the soil tillage system; soil fungal resources in annual cropping systems and their potential for management; nocturnal risks-high bat activity in the agricultural landscape indicates potential pesticide exposure. In this chapter, we have discussed the major effects of crop protection on biodiversity in detail regarding the persistence of biodiversity that needs to be mediated, considering the preserving of ecological properties and sustainable maintenance of biological integrity in agroecosystems. Farming systems, with their concerns of biodiversity, ecosystem services, and productivity and production issues towards progress in human needs, wellbeing, and sustainable development, are challenging in most biosphere reserves. In this book, a case study presented in last chapter assesses the levels and trends of the agro-biodiversity and ecosystem services of different farming systems in the Yayo Biosphere Reserve in Ethiopia.