The California Current system is a large marine ecosystem with transition gradients between subarctic and tropical biomes containing diverse habitats. Biogeographic species groups must be carefully analyzed in order to detect tendencies shifting the ecosystem toward a more temperate or tropical state. Species composition of hyperiid amphipods was analyzed in July 2002 for evidence of subarctic water intrusion and for signals of the El Niño event developing in the equatorial Pacific. Multivariate analysis showed a dominance of “transition zone” species typical of the California Current. The main evidence of subarctic water intrusion was the extended distribution of Themisto pacifica, which reached as far south as 27°N, with particularly high abundances at 30–32°N. The intrusion of subarctic water took place despite evidence that an El Niño event was in progress. The zonal advection due to El Niño intersected the equatorward flow of the subarctic intrusion and probably produced a large cyclonic eddy off Baja California. This eddy maintained a limited El Niño influence at a few offshore stations near its southern boundary. The main environmental variables influencing the amphipod assemblage structure were water temperature and the abundance of salps. T. pacifica, a species with cool water affinity, was more sensitive to temperature, whereas subtropical species, such as Vibilia armata, were strongly correlated with the availability of salps.