The diatom biochronology of ODP (Ocean Drilling Program) Holes 682A and 688E provides a detailed framework for refiningMiocene diatom zonation in the East Pisco Basin of southern Peru, establishing both a nearly complete offshore reference section and a correlation tool for the fragmentary onshore vertebrate-bearing deposits. This new biostratigraphic record documents a complete succession of low latitude and/or northeastern Pacific Miocene diatom zones, with two notable exceptions: a dissolution and/or hiatus interval (*16.5–14 Ma) during the Middle Miocene Climatic Optimum and a likely earliest Miocene hiatus (*23.4–21.8 Ma). Although eastern equatorial Pacific diatom zones characterize the Upper Oligocene and Lower Miocene strata, an increased abundance of cool-water diatoms that lived during the Middle and Late Miocene allows better application of northeast Pacific diatom zones, except during the Messinian (7–6 Ma) when warm-water diatoms predominate. The effects of eustatic sea level and tectonics on depositional sequences in the EPB and in offshore cores off central Peru are discussed.