Salps off Baja California (BC) showed substantial changes during El Niño of 1997-1998 and La Niña of 1998-1999. Salps were particularly abundant during the warm phase and showed a decreasing trend after the transition to cool conditions (October 1998). Salp swarms (>1 salp m -3) were present throughout the study period, with the exception of October 1999 and October 2000. They appeared more frequently S of Punta Baja (30°N). The most abundant species was Thalia orientalis followed by Salpa fusiformis. T. orientalis decreased in abundance from winter 1998 to autumn 1999, while S. fusiformis showed a strong increase during the development and establishment of La Niña (autumn 1998 and winter 1999). Other species (T. rhomboides, T. cicar, Cyclosalpa strongylenteron, C. polae, S. cylindrica and Ritteriella amboinensis) associated with warmer waters were present off the southernmost part of the BC peninsula. They were probably advected into the area from the SSW by an intensified coastal poleward jet that characterized the El Niño peak in the area. Estimates of carbon ingestion from daily rations of Thalia spp. and S. fusiformis indicated that swarms required from <1 to >100% of the daily primary production and phytoplankton biomass. Fecal pellet production of swarms of these species was estimated at between <1 and 609 mg C m-2 d-1. Considering that size and sinking rates of fecal pellets are related to salp body size, the swarms of Thalia and S. fusiformis may have had a differential impact on the pelagic ecosystem in terms of recycling and vertical transport of biogenic material through the water column. © Inter-Research 2006.