This article addresses the problem of definition and identification of clusters as localised mesoeconomic systems with fuzzy boundaries that stimulate the development of these systems. The author analyses the influence of the inductive approach to the formation of cluster theory and juxtaposes different typologies of clusters and other types of localised economic systems. The article offers an overview of the existing methodological approaches to the problem of cluster identification and emphasises the major role of institutional dimension in the identification (and functioning) of clusters, especially in comparison to cluster formation theory based on the technological connection of adjacent units. The author comes to a conclusion that, without the inclusion of institutional factors, alongside localising and technological ones (demonstrated through different variables), it is virtually impossible to develop an independent cluster theory, different from the general agglomeration theory. For the first time, a hierarchy of institutions affecting the formation of local economic systems is considered against the background of the identification of institutional levels, whose full development makes it possible to speak of the formation of clusters as most successful mesoeconomic systems. At the same time, the author emphasises that, in economies gravitating towards the market type of organisation, the development of mesoeconomic systems is closely connected to competition for innovative rent. The article outlines the methodology for cluster studies, which makes it possible to consider such relatively new to the regional science phenomena as innovative and “transborder” clusters.