Of the four major eastern boundary currents, the Humboldt Current (HC) stands out because it is extremely productive, dominated by anchovy dynamics and subject to frequent direct environmental perturbations of the El Niño Southern Oscillation (ENSO). The long-term dynamics of the HC ecosystem are controlled by shifts between alternating anchovy and sardine regimes that restructure the entire ecosystem from phytoplankton to the top predators. These regime shifts are caused by lasting periods of warm or cold temperature anomalies related to the approach or retreat of warm subtropical oceanic waters to the coast of Peru and Chile. Phases with mainly negative temperature anomalies parallel anchovy regimes (1950–1970; 1985 to the present) and the rather warm period from 1970 to 1985 was characterized by sardine dominance. The transition periods (turning points) from one regime to the other were 1968–1970 and 1984–1986. Like an El Nino, the warm periods drastically change trophic relationships in the entire HC ecosystem, exposing the Peruvian anchovy to a multitude of adverse conditions. Positive temperature anomalies off Peru drive the anchovy population close to the coast as the coastal upwelling cells usually offer the coolest environment, thereby substantially decreasing the extent of the areas of anchovy distribution and spawning. This enhances the effects of negative density-dependent processes such as egg and larval cannibalism and dramatically increases its catchability. Increased spatial overlap between anchovies and the warmer water preferring sardines intensifies anchovy egg mortality further as sardines feed heavily on anchovy eggs. Food sources for juvenile and adult anchovies which prey on a mixed diet of phyto- and zooplankton are drastically reduced because of decreased plankton production due to restricted upwelling in warm years, as demonstrated by lower zooplankton and phytoplankton volumes and the diminution of the fraction of large copepods, their main food source. Horse mackerel and mackerel, the main predators of anchovy, increase predation pressure on juvenile and adult anchovies due to extended invasion into the anchovy habitat in warmer years. In contrast to these periods of warm and cold temperature anomalies on the decadal scale, ENSO events do not play an important role for long-term anchovy dynamics, as the anchovy can recover even from strong ENSO events within 1–2 years. Consequently, the strong 1972–1973 ENSO event (in combination with overfishing) was not the cause of the famous crash of the Peruvian anchovy fishery in the 1970s.