Planktonic ostracods are deep dwelling mesozooplankton that are diel migrators and detritus feeders. In the Humboldt Current region off Peru they are shown to be strongly influenced by El Niño conditions. Species composition and distribution were compared in day and night (vertically hauled 50-0 m Hensen Net) samples that were collected from three latitudinal zones (3°40' S-6°S; 9°S-12°S and 15°S-18°S) during 1998 (El Niño year) and in 2001 (a year with usual upwelling regime). Unexpectedly, ostracods diversity and abundance were much higher during El Niño than during the upwelling regime. Tropical species that normally occurred north of 6°S, spread southwards and increased in abundance; Euconchoecia aculeata was often dominant, particularly in coastal waters, and the frequency of occurrence of others increased throughout the entire region (e.g. Porroecia porrecta, Archiconchoecia striata). Conversely, Conchoecetta giesbrechti, a species associated with subsurface oxygen minimum waters, was more frequently found and in higher abundance during the upwelling regime in 2001. Thus, El Niño conditions apparently favor the occupation of the epipelagic zone by many halocyprid species advected in from tropical waters, possibly because the higher oxygen content in the subsurface waters enables these diel migrating species to survive better. Additional factors may be a consequence of the switch to a picoplankton production cycle, which results in more detritus being retained in the upper waters, and the sharp reduction in planktivorous fishes such as the anchovy which may reduce the predation pressure they experience. © 2007 Springer Science+Business Media B.V.