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Based on the data of the plant macrofossil and palynological composition of the peat deposits, the evolution and current state of polygonal peatlands were analyzed at the southern limit of continuous permafrost in the Pur-Taz interfluve. Paleoreconstruction shows that peat accumulation began in the Early Holocene, about 9814 cal. year BP, in the Late Pre-Boreal (PB-2), at a rate of 1 to 1.5 mm year−1. Intensive peat accumulation continued in the Boreal and early Atlantic. The geocryological complex of polygonal peatlands has remained a stable bog system despite the predicted warming and increasing humidity. However, a rather rapid upper permafrost degradation and irreversible changes in the bog systems of polygonal peatlands occur with anthropogenic disturbances, in particular, a change in the natural hydrological regime under construction of linear objects.