This dataset contains stable carbon (δ¹³C) and oxygen (δ¹⁸O) isotope measurements of the planktic foraminiferal species Morozovella crater, Acarinina soldadoensis, and Subbotina roesnaesensis from Ocean Drilling Program (ODP) Sites 198-1209 and 198-1210 (Shatsky Rise, subtropical Pacific Ocean). The samples span the interval from approximately 54.47 to 50.91 Ma across the Early Eocene Climatic Optimum (EECO). The dataset includes sample age model (from Westerhold et al., 2018), benthic carbonate reference isotope values (from Westrhold et al., 2020), and species-specific isotope measurements. These data allow comparisons of isotopic trends among species and provide a basis for reconstructing ecological and paleoceanographic changes during the EECO prolonged greenhouse conditions.