Based on the census data from 1989, 2002 and 2010, the article analyzes the evolution of the ethnic structure of the population of the post-Soviet Russia from the territorial perspective. The stability of the ethnic structure of the “Russian mega nucleus” and indigenization of the national regions are considered in view of the differences in migration trends during the two inter-census periods and the socioeconomic situation in the regions. The urbanization rate of major ethnic groups is an indirect indicator of the prospects of traditional “primordial” ethnic identities indifferent ethnic groups. Special attention is paid to new trends — an increase in the number of people refraining from answering the question about their ethnic identity or giving an unclear answer. Alongside serious census errors, this phenomenon can be a result of growing complexity of the ethnic identity structures and the processes of modernization, which occur at different rates in Russian and national regions. Based on the 2010 census data, the article analyses the differences in polyethnicity between the rural and urban population, which are accounted for by the historical background, particularities of regional development, settlement features, and migration processes of the past two decades.