We used a dataset assembled by the Peruvian Marine Research Institute (IMARPE) from 1961 to 2005, to examine the influence of seasonal, environmental (temperature and salinity), temporal (day-night and year) and location (north-south and on-off shelf) variables on the distribution and biovolume of zooplankton. Classification and regression trees (CART) showed that the zooplankton distribution can be divided into four time regimes: prior to 1974.5, 1974.5-1989.5, 1989.5-1997.5 and 1997.5-2005. These periods differ in overall biovolume but, more importantly, in having different spatial distributions of variables. Offshore-onshore, seasonal, diel and north-south patterns are all apparent in the temporal changes observed in zooplankton distribution. In the early period zooplankton biovolume was high throughout the Peruvian Humboldt Current Ecosystem, with enhanced biovolume in all seasons but winter. After 1974.5, biovolume was considerably lower. There was an increased difference between the shelf (lower biovolume) and offshore (higher biovolume), with a significant day-night effect offshore, due to diel migration and possibly diel catchability changes. After 1989.5, seasonal effects were more marked and biovolume appeared to be higher in the winter in the northern region. In other seasons, during the daytime, biovolume was highest farther offshore (greater than 65 km offshore of the 200-m isobath) and, during the night, higher after 1997.5 than before. We relate these changes in distribution and biovolume to changes in large-scale current patterns in different regimes and to the possible effect of the fishery in removing nutrients from the system. © 2008 The Authors.