Using the example of several districts of the Middle Angara region, the changes in the system of rural settlements in the taiga zone of the Irkutsk region in the period from the first All-Russian Population Census in 2002 after the collapse of the Soviet Union to the last one in 2021 are revealed. The system-dynamic analysis also touched upon the period of formation of regional settlement systems, which fell during the Soviet period and played a major role in their genesis. Geoinformation mapping and analysis of settlement systems were carried out at different levels: regional, inter-municipal, local, elementary. The results of the study revealed that functional changes affected the majority of rural settlements and occurred due to the loss of agricultural and forestry specialization of settlements, especially in the Bratsk region. The loss of production functions by rural settlements, combined with long-term depopulation, is changing the established settlement systems. Mainly the grassroots settlement systems (elementary and local) are disappearing. Only the centers of these former systems remain, the viability of which is ensured by the relatively high population of settlements, the safety of social infrastructure facilities, and the possibility of employment. In the future, changes in the structure of settlement systems will require administrative reform within municipalities under a reactive problem response scenario, which can be seen in the example of the Chunsky district, which has transformed into a district. For proactive actions by the authorities, it is necessary to stimulate the development of small and medium-sized businesses, covering the fields of specialization of the research areas, and the formation of new industries.