In this dataset, we provide pollen counts of 5 permafrost sediment samples from the Batagay megaslump, Yakutia. For each sample, 2.85-4.58 g of wet sediment was taken for pollen preparation. A standard preparation method including KOH, HCl, HF, and acetolysis was used. At least 300 pollen grains and spores were counted in each sample except for B17-D3_MIS17-16, where only 178 palynomorphs were counted. Detailed method is described in Courtin et al., 2022.