The Pisco Formation is a Mio-Pliocene formation cropping out for 300 km along the coast of Peru. This mainly diatomaceous formation is famous worldwide for being a fossil marine vertebrates Lagerstätte. Diatom biostratigraphy was applied to date the Pisco Fm. in few previous works (Macharé et Fourtanier, 1987; Schrader et Ronning, 1988; Koizumi, 1992); those works applied species ranges used in both the Cenozoic middle- to high-latitude North Pacific zonation and Cenozoic low-latitude zonation of Barron, 1985. During recent fieldworks stratigraphic sections at Cerro Colorado and Cerros Los Quesos (Ica desert, Peru), were measured and samples for biostratigraphy were collected ca. every 5 m. Difficulties arose during the biostratigraphic investigations because of the paucity of index species: indeed, coastal and upwelling conditions, which characterized the two sites, lead to the proliferation of species with long stratigraphic ranges such as Odontella aurita, Rhaphoneis spp., Delphineis spp., Coscinodiscus spp., Chaetoceros spp., etc. Results were obtained merging together ranges of species used both in the equatorial Pacific and in the North Tropical Pacific schemes. Cerro Colorado is characterized by an angular discordance that divides it into a lower and an upper allomember (Di Celma et al., 2015). The co-occurrence of the diatom species Denticulopsis hustedtii and Lithodesmium reynoldsii allows the attribution of the lower allomember to the late Miocene, while the only index species present in the upper allomember is Thalassiosira antiqua, which has a stratigraphic range that goes from the late Miocene to the late Pliocene. Thus samples from the upper allomember alone do not permit an accurate dating of the post-discordance sediments. The base of the Cerros Los Quesos sequence is characterized by a younger form of T. antiqua, differring from that of Cerro Colorado by having a more regular central area. Therefore, speculations on the time-relationship between the two sites can be made based on differences in T. antiqua. The presence of many plicated Thalassiosira specimens ascribable to Thalassiosira flexuosa, suggest that Cerros Los Quesos, although younger than Cerro Colorado, is still late Miocene in age.