ABSTRACT: Boundary currents influence near-shore ecosystems worldwide, and understanding how fish assemblages change spatially and temporally throughout these systems is important for establishing the scale at which ecosystem-based management (EBM) should be conducted. Because most research on boundary currents in general, and the California Current System (CCS) in particular, have been restricted to only small portions of the systems, it is largely unknown whether fish assemblages in boundary currents form one coherent ecosystem or if changes in assemblage structure are locally independent. We expand the geographic scope of previous analyses on ichthyoplankton assemblages within boundary currents by comparing dynamics in 2 widely separated regions of the CCS: Oregon (~45°N) and southern California (~34°N) in spring and summer from 2004 to 2011. Both region and season affected assemblage structure. Some taxa that were moderately common in California were consistently rare or absent in Oregon (and vice versa), and the presence of most decreased in summer in both regions. However, the assemblages were very similar in some years. Off Oregon, the assemblage most resembled California’s when the ocean temperature was relatively high and northern anchovy Engraulis mordax was abundant. Assemblage dynamics were well explained by environmental change in Oregon. By contrast, California’s assemblage and environmental variability correlated poorly. Population sizes of taxa common to both regions did not fluctuate coherently in Oregon and California. These findings are important for EBM because they indicate that it is not possible to extrapolate results from spatially restricted localities to understand assemblage dynamics throughout the entire CCS.