The El Niño event of 1997/1998 provided an opportunity to carry out a field experiment in which the relationship of sea surface temperature and the association of Vibrio cholerae with marine plankton could be assessed in Mexican coastal and estuarine areas. Plankton samples were collected from May 1997 through June 1999. Sites included the Mexican ports of Veracruz, Coatzacoalcos and Frontera in the Gulf of Mexico and Ensenada, Guaymas, Mazatlán, Manzanillo, Acapulco and Oaxaca in the Pacific Ocean. Sampling was also accomplished during two oceanographic cruises in the Yucatan channel of the Caribbean Sea. Bacteriological analyses for V. cholerae serogroups O1 and O139 were carried out. Also, the taxonomic structure of the plankton populations was determined. Vibrio cholerae O1 was detected only in Veracruz samples collected during April, May and June 1999, when La Niña climatic conditions prevailed. It is concluded that V. cholerae O1 in Mexico derives from its marine and estuarine origin and not from sewage contamination. The significant number of Acartia tonsa copepodites and V. cholerae copepodite-positive samples suggests a significant role of this copepod in the occurrence and distribution of V. cholerae in coastal areas of Mexico.