The dataset contains metagenomic 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 42 samples) were extracted using the DNeasy PowerMax Soil Kit (Qiagen, Germany) and were pepared with a single-stranded library protocol for NGS sequencing on a NextSeq2000 sequencing system (ilumina) using the NextSeq 2000 P3 Reagents and 2x100 pairedend mode. The raw sequencing data was demultiplexed and the sample specific R1 and R2 DNA data files are provided. The dataset contains R1 and R2 raw read files from 42 sediment core samples covering a time period between 1820 and 123340 cal years BP and additionally 13 blank controls, which served has lab controls during extraction and library preparation.