The dataset contains amplicon DNA raw sequence files from the marine sediment core SO201-2-77KL sampled in the Western Bering Sea. Approximately 7 g of each sediment sample (in total 54 samples) were extracted using the DNeasy PowerMax Soil Kit (Qiagen, Germany) and were pepared for NGS amplicon sequencing by using PCR amplifications with tagged primers rbcl_705 and rbcl_808 and a PCR-free library protocol. NGS sequencing was condcuted on a NextSeq sequencing system (illumina) using the NextSeq Mid kit in 2x150 pairedend mode. The dataset contains of a R1 and R2 raw read file which contains amplicon-sequences from 3 replicates of 54 sediment samples (totally 162 PCR samples) covering a time period between 1820 and 123340 cal years BP samples and 40 blank controls.