The California Current region encompasses a gradient between coastal upwelling and oligotrophic offshore zones, where the phytoplankton biomass is dominated by species of large and small celled phytoplankton, respectively. Mesoscale eddies are ubiquitous in the mixed region between the coastal and offshore zones, and they mediate the offshore transport of coastal waters. Mesoscale eddies are known to trap and transport water masses and their associated biogeochemical signatures, acting much like traveling mesocosms. It is unclear to what extent phytoplankton communities are trapped by the eddies, and how much they mingle with the communities found in the surrounding waters. In this study we characterized the phytoplankton community structure found within three mesoscale eddies, two cyclones and one anticyclone, using flow cytometry and 16S and 18S tag sequencing. We tracked the age and region of formation of the eddies from sea surface height. The two cyclonic eddies were formed in the same region, but at different times, C1 was 22 days old and C2 was 214 days old at the time of sampling. The anticyclonic eddy, A1, was formed further to the south and was 19 days old at the time of sampling. We assess to what extent the phytoplankton communities within each of the eddies are distinct from their surrounding waters, differ from each other, and how much the phytoplankton communities vary within each of the eddies with distance and depth. Our results show that the phytoplankton community is structured, to first order, by the physical environment, such that the phytoplankton metacommunities differ between eddies. However, we also see finer scale features with community changes within and across the eddies. These deviations reveal patchiness in the communities likely driven by corresponding local patchiness in nutrient and trace metal concentrations.