This study monitored the abundance of the tropical/subtropical seaweed Caulerpa sertularioides (Chlorophyta: Bryopsidales) from a sandy beach from Balandra Cove, on the south-eastern coast of the Baja California Peninsula, Mexico, between April 1998 and April 2000, including consecutive El Niño and La Niña events. El Niño conditions, indicated by relatively high seawater temperatures, were associated with a high population abundance (April–June 1998), whereas La Niña conditions, indicated by relatively low temperatures, were associated with the absence of C. sertularioides (April–June 1999 and April 2000). Caulerpa sertularioides was present during other times of the year during the study period, but never with the high abundance reached during El Niño conditions. Seaweeds of temperate affinity occurring in Baja California, such as Gelidium robustum (Rhodophyta: Gelidiales) and Macrocystis pyrifera (Phaeophyceae: Laminariales), decreased sharply in abundance during El Niño conditions. Therefore, the biogeographic affinity of seaweeds from Baja California might be helpful in predicting the effects of El Niño and La Niña on their abundance, with implications for resource management and for the prediction of the effects of long-term oceanographic changes on seaweed distribution.