We examined the changes in four intertidal macroalgal assemblages sampled at 3-month intervals during and after the 1997–98 El Niño. The assemblages were analyzed using several numerical analyses (specific richness, H′ diversity) and multivariate techniques (ANOSIM, cluster, and MDS analyses). During El Niño 1997–98, the water temperature in the sampled zone was almost 5°C above the long-term mean. The apparent impact of this factor was greatest in winter–spring 1998. Our results suggest that El Niño influenced the structure of these assemblages in four different ways: (a) El Niño was associated with number of species (lowest in 1998) and H′ diversity, which increased in the winter of 1999, when the El Niño–Southern Oscillation (ENSO) was inactive, from 1.2 to 2.3. (b) The average biomass of the macroalgae was significantly greater in the ENSO year (139 g dry weight/m²) than in the non-ENSO year (42 g dry weight/m²) (c) El Niño conditions were associated with a high population abundance of species of tropical affinity, such as Agardhiella tenera (22.05 g dry weight/m² in 1998 versus 0.7 g dry weight/m² in 1999), Amphiroa misakiensis (32 versus 1.1), Caulerpa sertularoides (15.35 versus 0), Padina durvillaei (9.2 versus 0.2), Jania capillacea (4.1 versus 0), and Jania mexicana (1.5 versus 0). In 1999, other species with a more temperate affinity appeared, such as Laurencia pacifica (0.12 versus 8.76 g/m²) and Colpomenia sinuosa (0 versus 4.8). (d) The multivariate techniques showed that differences among the structure of the four assemblages were more evident in 1999. The greatest homogeneity was detected during ENSO winter–spring, which suggests a communitywide change consistent with the El Niño event.