An integrated approach is applied in the study to define the concept of ecosystems and features of their development in current conditions. Three groups of ecosystems are identified and a number of their types are defined, including industrial, agro-industrial, agrarian, entrepreneurial, social, innovative, national, university, regional, corporate, sectoral and business systems. The understanding of clusters as a transitional form of ecosystems is grounded, the author’s classification of them is proposed. The concept of a cluster is connected, first of all, with the phenomenon of spatial economy, therefore, the essential characteristics of spatial economy are defined in the paper. The systematization of the viewpoints of various scholars is presented along with the author’s approach to the classification of clusters according to different criteria. The problematic field of creation and development of innovative clusters in the field of agriculture is presented. The list of participants of innovative clusters in the agro-industrial complex and the system of relations between them in various functional areas are studied, and also promising trends in terms of digital economy are substantiated.