The United States and Mexico share the Southern California Bight (SCB) ecosystem in the Northeast Pacific Ocean where marine wildlife and habitats historically have been disturbed by human activities. Within this ecosystem, forests of the giant kelp Macrocystis pyrifera are critical habitats that sustain diverse biological assemblages and important fishery species. We studied patterns of temporal and spatial variability within the benthic communities of five transboundary kelp forests in California (USA) and Baja California (Mexico) over a fouryear period that included a moderate El Niño event. While the benthic marine communities shared some species, they varied significantly in community structure from each other, and the degree of dissimilarity was not related to the geographic distances among the studied habitats. Rather, species richness was significantly related to local substratum rugosity, suggesting it could be used as a proxy of relative benthic biological diversity. Temporal changes in the benthic assemblages were not consistent across all forests, and contrary to observations made during previous El Niño events in the SCB, the benthic communities did not change significantly following the 2009-2010 El Niño. Such an unexpected community response may be explained by the fact that the 2009-2010 El Niño was linked to the Modoki phenomenon, where warm sea surface temperature is focused in the central equatorial Pacific and not in the eastern Pacific Ocean. We propose that long-term conservation efforts should incorporate this ecological knowledge to support science-based decisions, binational coordination of policies, and coherent management practices including the design of transboundary conservation networks as spatial management tools for the protection, conservation, and/or restoration of the SCB ecosystem. [ABSTRACT FROM AUTHOR]