The Mio-Pliocene Pisco Formation, Peru, is a world renowned Konservat-Lagerstätte. Beside its potential in preserving important information on the history of the Pacific Ocean during the Miocene, the Pisco Fm. provides palaeontologists with the unique opportunity to study in detail the evolution of marine vertebrate fauna during the Neogene. Because diatomites are one of the main lithologies of the Pisco Fm., previous authors have hypothesised exceptionally high sedimentation rates related to the deposition of diatom frustules as the main cause leading to the formation of the Lagerstätte. However, sedimentation rates were never calculated. With the perspective to build a solid stratigraphic framework for the whole Pisco Fm., we started to investigate two important fossiliferous sites: Cerro Colorado and Cerro Los Quesos. Within these two areas, measurement of multiple stratigraphic sections combined with extensive field mapping of a number of distinct marker beds was carried out, which allowed a high-resolution correlation and creation of a local lithostratigraphic framework. Integrated tephrostratigraphy, 40Ar/39Ar dating and diatom biostratigraphy permitted an accurate chronostratigraphy to be established. Both biostratigraphic and radiometric ages converge to indicate a late Miocene age for the two sites, amending previous attribution of Cerro Colorado and Cerro Los Quesos to the middle Miocene. Age models for the site of Cerro Los Quesos reveal that sedimentation rates are high but in line with those of high-productivity environments, thus invalidating the hypothesis of exceptional sedimentation rates as the main cause for the formation of the Lagerstätte. These results are extremely important also in the perspective of building a complete stratigraphic framework for the Pisco Fm.