Changes in abundance and distribution of anchovy and other species of pelagic fish of the Northern Humboldt Current System (NHCS) are driven by environmental forcing variations in different time and spatial scales between the coastal 'cold' ecosystem and the 'warm' oceanic one. Data to study these fluctuations have come mostly from the fishery to show how anchovy (Engraulis ringens) increases when sardine (Sardinops sagax) declines and vice versa. However, using acoustic data on latitudinal biomass we show that other species as mackerel (Scomber japonicus) and jack mackerel (Trachurus murphyi) also follow the same opposed trend, then the fishery data hides the true dimension of the balance of abundance among species. Based on Hovmoller diagrams we scrutinized the changes in interannual latitudinal acoustic biomass, landings and influence of El Niño events from 1966 to 2009 in order to describe: 1) how the anchovy decadal distribution pattern moved from south to north since the 1960's; 2) how there have been produced concomitant changes in the latitudinal abundance and distribution of other species such as sardine, jack mackerel and mackerel before, during and after El Niño events; and 3) what was the overall effect of the succession of El Niño events on all these pelagic species. We concluded that: a) every El Niño event has had an effect on the expansion or contraction of pelagic species distribution and abundance, with different latitudinal effects; and b) the El Niño 1997-98 did not trigger but accelerated a decline phase on the abundance of sardine, jack mackerel and mackerel by a reduction of their ideal habitat due to an expansion of the coastal ecosystem caused by a shallower location of the upper limit of the Oxygen Minimum Zone (OMZ) These findings observed using past data might be taken into consideration for fishery management purposes when considering future scenarios.