Cenozoic sediments are spread across southeast and eastern Anatolia, including the Adıyaman–Malatya regions of southeast Turkey. This study presents the first detailed petrographic, micropaleontologic, and strontium isotope analyses of the Eocene marl, clayey limestone, and limestone units that outcrop unconformably above the Mesozoic Meydan and İspendere ophiolitic rocks in the Adıyaman and Malatya regions, respectively. These carbonate rocks contain abundant planktonic foraminifera, including Turborotalia frontosa, Subbotina senni, Subbotina eocaena, Acarinina bullbrooki, Guembelitrioides nuttalli, Globigerinatheka subconglobata, and G. curryi, and benthic taxa (Nummulites, Discocyclina, and Chapmanina).Two planktonic foraminiferal zones were defined: the Turborotalia frontosa zone representing the Early–Middle Eocene (Ypresian–Lutetian/Bartonian), and the Turborotalia possagnoensis zone representing the Middle Eocene (Lutetian–Bartonian). Strontium isotope ratios (87Sr/86Sr) calculated for four samples ranged between 0.707663 and 0.707784, indicating an age of 45.1–51.9 million years (Ypresian–Lutetian/Bartonian). The presence of echinoid thorns in the units indicates a shallow marine environment where carbonates developed on the seaward side of a reef. For the first time in the study region and southeast Anatolia, this study has revealed the stratigraphic position of the Nummulitic limestone of the Kırkgeçit Formation unconformably overlying the ophiolites. Therefore, based on strontium isotope analyses and planktonic foraminiferal micropaleontology, the Kırkgeçit Formation is estimated as Early–Middle Eocene (Ypresian–Lutetian/Bartonian) in age.