The 20th century urbanization development processes led to the transition from local urban forms to area formations or agglomerations. They became the prime engine of social and economic development. This is also true for Russia: throughout its history, cities have been the centres of its spatial organization. The transition to market economy has actualized the problems of agglomerations research in Russia: they are the basis for the formation of regional and national competitiveness. At this time, a number of agglomerations has been studied in bits and pieces or scarcely researched. One of such agglomerations is the city of Yakutsk, forming the largest agglomeration in the north-east of the country. The study of agglomeration development of Yakutsk is relevant for a number of reasons: as the center of the largest region, it is inextricably linked with it in its development, forming both opportunities and problems, and at the same time it is located in difficult natural and climatic conditions on the territory of perennially frozen rocks. This article is dedicated to history of the agglomeration formation, its specific and essential features. The theoretical and methodological background of the urban agglomeration formation and functioning as a specific spatial structure including the main factors of growth and development of agglomeration firstly were considered. The article noted that a range of issues about the Yakutsk agglomeration have not yet been studied despite their expressed relevance: the agglomeration structuring, allocation of different functional zones; processes of formation and development of the city structure; positive and negative sides of the urban agglomeration development; the issue of boundary delineation and selection of methods for this operation.