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New age estimates obtained via Strontium Isotope (87Sr/86Sr) Stratigraphy and new paleoclimatic data are here presented for the Miocene Chilcatay and Pisco formations exposed in the East Pisco Basin, an Andean forearc basin of southern Peru, which is renowned worldwide for its exceptional content of fossil marine vertebrates. Mollusk and barnacle shells, carbonate nodules, and shark teeth were collected along three stratigraphic sections for applying Strontium Isotope Stratigraphy on both carbonates and phosphates. To avoid diagenetic biases, mollusk and barnacle shells were analyzed in detail by means of optical and scanning electron microscopy, cathodoluminescence, and inductively coupled plasma-optical emission spectrometry, whereas only the enameloid from the best-preserved shark teeth was sampled. The obtained 87Sr/86Sr ages confirm a late early Miocene (Burdigalian) age for the Chilcatay strata, and reveal middle Miocene (Langhian to Serravallian) ages for the lower Pisco unit (i.e., the P0 sequence) – a result that matches the relatively archaic aspect of its cetacean fossil assemblage. New and literature data about the fossil assemblage of the lower Pisco beds highlight the presence of several thermophilic invertebrates and vertebrates, thus suggesting a warm-water, tropical paleoenvironment for this middle Miocene sequence. Such a paleoenvironmental scenario recalls the warm conditions associated with the Chilcatay Formation, rather than the cooler setting inferred for the remainder of the Pisco Formation (i.e., the P1 and P2 sequences). This pattern likely reflects the late Miocene trend of global cooling, as well as a middle to early late Miocene strengthening of the Humboldt Current.