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ENSO significantly changed the annual patterns of rainfall and temperature for northwestern Mexico. Little is known about how seasonal environmental differences influence the long-term pattern of distribution and density of rodents in desert habitats of North America. We report data from a long-term study (October 1994-December 1999) of two areas west of La Paz, Baja California Sur, Mexico. One is a natural preserve and the other is grazing land. Both have the same original vegetation, soil, and weather. Densities of rodent populations in both areas were compared. El Niño’s impact in La Paz region did not increase rainfall, as in other areas of Mexico. In the grazing area, monthly anomalies of rodent density showed a significant impact from the ENSO event, but the preserve showed less impact. Rodent population variations can be related to the precipitation effect. In the grazing area, the effect is much stronger. During the rainy season, population increases, but in the dry period, the population strongly declines. The effect lasts many months, and is related to the reduced number of perennial species. For altered desert areas, the dry season of ENSO was the most significance part of the event.