This dataset contains bulk organic matter and biomarker data for two Mediterranean Sea sites: ODP Leg 160 site 964 (including sapropels S5, S7, and i-282) and ODP Leg 160 site 967 (including sapropels S4, S5, and S74). This dataset includes: (i) compiled age model data from the literature; (ii) diagnostic mass spectrometry selective reaction monitoring m/z ratios for bacteriohopanepolyol (BHP) and heterocyst glycol (HG) analysis; (iii) bulk sediment % organic carbon (OC), % total nitrogen (TN), OC-d13C, and TN-d15N; (iv) OC-normalized abundances of various BHPs, HGs, and crenarchaeol; (v) d13C values for BHPs and crenarchaeol; and (vi) literature compilation of Eastern Mediterranean Sea diatom frustule preservation observations. Samples were analyzed at Harvard University in 2017-2018 from samples collected in 1995 during ODP Leg 160; sample ages range from 101 to 3004 kilo years before present. Samples were collected from the Eastern Mediterranean Sea and cover the Ionian and Levantine Seas. These data were generated to study the microbial ecological and biogeochemical responses to ocean anoxia in an enclosed basin; samples were analyzed using mass spectrometric and isotope-ratio mass spectrometric methods (coupled to liquid- and gas-chromatography and elemental analysis).This work was supported by the Gordon and Betty Moore Foundation.