Traditional microscopy has long been used to identify plankton communities and estimate their biomass. The widespread use of next-generation molecular methods in recent years has revealed the incredible diversity of planktonic microbes at the base of the marine pelagic food web, particularly with respect to pico- (0.2 -2 µm) and nanoeukaryotes (2-20 µm). We present data from samples collected in the southern California Current Ecosystem (CCE) on plankton diversity and biomass determined from both microscopy analyses and 16S and 18S rRNA amplicons. Distinct patterns in community biomass (µg C L-1) and diversity (Shannon index) appear with respect to sampling depth (surface versus chlorophyll max) and distance to shore (coastal versus offshore). Differences in the level of diversity and the taxonomic composition of plankton communities across trophic gradients and over time opens new avenues for investigating patterns in community succession in this highly productive region.