The data set contains census counts of deep-sea benthic foraminifera from the Holocene section of sediment core GeoTü SL99. Given are counted individuals of benthic foraminiferal taxa versus sediment depth in cm below sea floor. The counts are based on representative splits of the size fraction >125 µm. The original counting was performed in 2020, a taxonomic revision was carried out in 2022. Gravity core GeoTü SL99, was retrieved at station no. 564 during R.V. METEOR cruise M51/3 in 2001 (Hemleben et al., 2003) from the southwestern Levantine Basin in the eastern Mediterranean Sea, at 33°00.0'N, 23°37.6'E, 1476 m water depth, core recovery 5.32 m. The sediment core was retrieved for the reconstruction of circulation and productivity changes in the eastern Mediterranean Sea during the late Quaternary with particular focus on sapropel formation.