Within the southern California Current ecosystem there are two well-documented breaks in marine community structure at Point Conception and Punta Eugenia. We explored the presence of similar breaks in a diverse zooplankton community through metabarcoding of mixed net tow tissue samples collected during an expedition from Monterey to Baja California in February of 2012. We recovered a high diversity of species as well as patterns of species presence that align with their previously documented ranges in this region. We found a clear break at Punta Eugenia in overall zooplankton community structure, while Point Conception was weakly linked to changes in community structure. We analyzed this dataset through two parallel bioinformatic pipelines to examine the robustness of these results. Our overall conclusions were consistent across both pipelines, however there were differences in species detection. This study illustrates the utility of metabarcoding analysis on mixed tissue samples for recovering known patterns of diversity, as well as allowing elucidation of broad patterns of community differentiation across many groups of organisms.