The agro-biodiversity present in agro-ecosystems is fundamental in guaranteeing sustainability and resilience. However, there are very few proposals for evaluating it and, even less, ones that include indicators to analyze the influence of the structural and spatial configuration of a landscape in order to favor agro-biodiversity connectivity to productive systems, management and conservation practices, and the producer (farmer)’s perceptions, awareness and ability to favor it on his farm. The Main Agro-ecological Structure MAS is redefined as an environmental agro-biodiversity index. New indicators are established for a total of 10 criteria and 29 indicators of systems that describe the agro-biodiversity of agro-ecosystems. Methodologies for its evaluation are also described, and the possibility of adapting certain indicators according to the ecological and cultural contexts where the farms are located is discussed.