Arid ecosystems of western South America that are affected by ENSO events experience short-term pulses in precipitation that trigger changes in the recruitment and growth of vegetation. We hypothesized that strong ENSO events, such as those of 1982/83 and 1997/98, could influence animal communities over several decades. We surveyed populations of three sympatric species of geckos (Phyllodactylus spp.) at the Illescas Peninsula, northern Peru, in 2004, and compared our results with those collected by Huey [1979. Parapatry and niche complementarity of Peruvian desert geckos (Phyllodactylus): the ambiguous role of competition. Oecologia 38, 249-259] in 1968. We found that the number of mesquite trees was much higher in 2004 than it was in 1968. The frequency of the most arboreal species of gecko, Phyllodactylus reissi, was higher in 2004 than it was in 1968. P. reissi was also more likely to be associated with mesquite trees in 2004 than in 1968. Carbon and nitrogen stable isotopes could not be used to identify the most important source of primary productivity for the diet of geckos, because the values of mesquite trees and Capparis shrubs were similar. However, nitrogen isotopic values suggested that one species of gecko was incorporating marine-derived nutrients in its diet. © 2007 Elsevier Ltd. All rights reserved.