The paper focuses on the anatomy of the ethno-political transformations of the unique administrative unit of the Tajik Soviet Socialist Republic during the late Perestroika period (1989–1991). The research object is the Kūhistoni Badakhshon Autonomous Region (GBAO or simply the Pamirs). The subject being analyzed is the response to the massive crisis of the dissolution of the USSR by the exceptional sociopolitical system of the Soviet Pamirs. The core of the sources for the study was made up of documents and write-ups from the State archive of Kūhistoni Badakhshon Autonomous Region named after Kh. Buribekov (town of Khorugh, Tajikistan). These funds reflected the activities of main local political institutions, such as the Regional Soviet of the people’s deputies, Executive Committee of GBAO, the Supreme Soviet of Tajikistan and its Presidium. The information from the national and regional press was also examined. On the basis of a wide range of sources it has become possible to reconstruct the features of administrative and social disorganization of the autonomous region as well as the key aspects in its search for new prospects. The “dissection” of the political transformations in the Pamirs in 1989–1991 enabled the scholars to conclude that the project of sovereignization of GBAO was unfeasible for many reasons, such as cultural antagonisms inside the region; discord among the “old” communist elites over the act “On GBAO” and declaration of the republic; economic dependency on the Soviet centre; passiveness of the “ethnic Pamiri” in the republic administration of Tajikistan. The main external factors which should be emphasized were the influence of the conflict in Afghanistan and the absence of the support from “democratic” elite of the RSFSR.