Interannual and regime (decadal) scale changes in climate affect the spatial distribution and productivity of marine fish species in numerous ecosystems. We analyzed a historical simulation (1965-2000) from an end-to-end ecosystem model of anchovy population dynamics for the California Current System to untangle the effects of warm versus cool conditions on recruitment. A�3-dimensional coupled hydrodynamic-NPZD (nitrogen-phytoplankton-zooplankton-detritus) model (ROMS-NEMURO) provided the physical conditions (circulation, temperature) and 3 zooplankton concentrations as inputs to an anchovy full life cycle individual-based model (IBM). Our analysis was focused on isolating the effects of the well-documented El Niño Southern Oscillation signal and 3 climate regimes on spawning habitat, development, and survival of eggs and yolk-sac larvae, growth and survival of larvae and juveniles, and ultimately recruitment of anchovy. The major drivers of lowered recruitment success in warm years and in warmer regimes were reduced survival and growth rates of eggs and larvae that resulted from the poleward shift of adults in response to warmer temperatures prior to spawning. Three model-data comparisons showed the model deviated from empirically derived values of annual recruitment success but agreed with data for annual mean latitude of egg distributions and predicted larval consumption rates versus measured zooplankton concentrations. More effort is needed to improve certain biological aspects of the IBM so that it can replicate empirically estimated recruitment fluctuations. Overall, the altered responses of anchovy to changing climate in the California Current domain illustrate the benefit of the present mechanistic approach to infer how anchovy may respond under future ecosystem conditions.