Clustering of economic activity is an issue of particular interest for regional studies and economic geography, as well as an important practical task faced by Russian regions and related to the enhancement of competitive capacities. The aim of the study is to capture the current trends in the formation and development of clusters across the coastal regions of the European part of Russia, to determine the nature and degree of interdependence between the innovation, coastal, and agglomeration factors. The study is focused on the methodological aspects of studying the interrelation of the agglomeration space and the dynamics of cluster initiatives under the influence of coastalization. The study takes into account institutionalized clusters and de facto operating ones which have formed over the past two decades in the Rostov, Kaliningrad, Leningrad, Murmansk and Arkhangelsk regions, Krasnodar Krai, the Republics of Karelia and Crimea, Sevastopol and St. Petersburg. There have been identified the features (both advantages and problems) of the cluster development in coastal agglomerations, which are the foci of early clustering in the regions under consideration. In the context of increasing geo-economic instability, the factor of coastal location and external technological dependence initiated the innovation vector in shaping the cluster specialization, including in maritime sector, focused on import substitution.