Tephra layers are a unique tool for stratigraphy. Their geologically instantaneous deposition across wide areas makes them a powerful instrument for dating and correlating distant localities. In this paper, we apply tephra fingerprinting for high-resolution stratigraphic purposes in the upper Miocene portion of the Pisco Formation, which crops out along the southern Peruvian coast. The Pisco Formation diatomaceous strata host an important marine vertebrate Fossil-Lagerstätte, whose palaeontological relevance has entailed the necessity of reconstructing a detailed chronostratigraphic framework using 39 Ar– 40 Ar dating and tephra correlations. Distal ashes from the Central Andes volcanoes are frequent in the Pisco Formation, but their similar glass composition and mineral assemblage, together with the shallow marine environment limiting tephra preservation, could be unpromising for tephra-based correlations. In this study, tephra layers from measured stratigraphic sections were fingerprinted with a combined petrographic and microanalytical approach, including glass shard morphology and granulometric analyses. Based on the obtained results, we correlated sections several kilometres apart, greatly increasing the chronostratigraphic detail. Major element composition of biotite proved a valuable tool to discriminate the Central Andes metaluminous to peraluminous tephra deposited in the Peruvian forearc basins. This study highlights the applicability of tephra fingerprinting in unfavourable shallow marine environments.