Monitoring essential marine biodiversity variables is an effective means for assessing impacts of climate change and human-related stressors such as pollution, overfishing and habitat destruction. Yet little is known about the natural variability of biodiversity in pelagic upwelling marine ecosystems, which are often subject to substantial interannual and decadal variability of ocean climate conditions. Using data from a pelagic midwater trawl survey, we quantified diversity indices of epipelagic forage species collected over 26 yr (1990 to 2015) to determine the natural variability and environmental determinants of biodiversity within the California Current upwelling ecosystem. Biodiversity time series indicate there are 2 alternate forage species assemblages that relate to differences in cool/strong and warm/weak upwelling years that vary in 3 to 5 yr cycles. Cooler years are associated with increased biodiversity of juvenile groundfish, whereas warm years coincide with increased biodiversity of coastal and mesopelagic fishes and species originating from southern and subtropical waters. During 2015, a year of anomalous warm surface ocean conditions, we observed unprecedented high levels of biodiversity and attribute it to high abundance of juvenile groundfish combined with an unusually high transport of subtropical and offshore species into neritic waters. Using a combination of remote sensing and in situ hydrographic data, we compare 2015 to previous anomalous ocean climate conditions and discuss how biodiversity of forage species may impact trophodynamics of upwelling ecosystems and predator−prey interactions. Attributing changes in marine biodiversity to productivity cycles and anomalous climate events, and detecting long-term biodiversity trends, provides a critical index toward understanding climate forcing on upwelling ecosystems.