The objective of the present study was to verify possible spatial, seasonal, and inter-annual changes in the zooplankton off Paita (northern Peru), an upwelling area located closely to the limits of cold Humboldt Current and warm Equatorial Surface Waters. Zooplankton was sampled at subsurface on 53 occasions from August 1994 to December 2004 at four stations located 2 to 30 km offshore with a WP-2 net (300 μm). Extremely high surface water temperatures combined with low salinities were observed during the 1997/98 El Niño up to 29.0 °C) and in April 2002 (up to 25.0 °C). Temperatures more than 2 °C above monthly average were also observed in October 1994, in April 2000, and in November 2004. Significant trends were observed for oxygen concentration (increase) and several horizontal and vertical gradients. Among the copepods (72% of all individuals), the most abundant species were Paracalanus parvus (28%), Acartia tonsa (26%), and Calanus sp. (10%). The strong 1997-98 El Niño (EN) event led to drastic changes in species composition that were reversed during the 1998-99 La Niña (LN) event. Community parameters such as total abundance, diversity, equitability and species richness displayed marked variations associated with the 1997-98 EN and long-term trends. Long-term trends were significant for several vertical and horizontal temperature and oxygen gradients, indicating an increase in upwelling intensity at the shelf during the study period. 10-year-trends were also significant for total zooplankton abundance (increase) and community evenness (J, decline). Our data confirmed the importance of the weak EN in 2002/03 for the study region. Within the trend of increasing zooplankton abundance, a sharp step or shift was observed from 1999 to 2000. When using sequential t-tests to detect shifts in (x + 1) transformed abundance data, a significant rupture was found between the last sampling in 1999 and the first sampling in 2000. Also, a substantial decrease in diel variability occurred after 1999, probably due to changes in vertical migration patterns. The considerable increase in zooplankton abundance over the study period, the ENSO effect, and the 1999-2000 transition are discussed with regard to synchronicity with other zooplankton time series. The present study contributes with the first evidence from an important area located in the Humboldt Current for synchronous trends and changes that were previously observed elsewhere in the Pacific. Our results demonstrated the importance of long-term zooplankton monitoring studies in upwelling areas, and confirms the idea of dramatic changes in pelagic ecosystem structure occurring in the East Pacific. © 2009 Elsevier B.V. All rights reserved.