In 2013 a coring campaign was carried out as part of the project Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) and under the umbrella of the International Continental Scientific Drilling Program (ICDP). A 584 m sediment succession was retrieved from the central part (DEEP site) of ancient Lake Ohrid at a water depth of 243 m. The upper 446.65 mcd that represent the entire lacustrine history back to ca. 1.363 Ma contain a remarkably well-preserved record, especially of planktonic diatoms. We here present the count data of planktonic diatoms from core ICDP5045-1 spanning the period from 1.363 Ma until present. Diatom count data were generated from 350 sediment samples taken at a temporal resolution of 2.0–4.0 ka and each slide was analysed across random transects to count 200–400 diatom valves.