In southern California the Dulzura kangaroo rat (Dipodomys simulans) occurs in shrub-dominated habitats adjacent to forb- or grass-dominated habitats, which support the endangered Stephens's kangaroo rat (D. stephensi). We monitored a number of populations of both species from 1996 through 2000, spanning the 1997–1998 El Niño Southern Oscillation (ENSO) event. Although populations of D. stephensi were not significantly impacted by this climatic event, D. simulans declined from 10–24 individuals/ha to about 7–12 individuals/ha over a 6- to 8-month period; numbers subsequently continued to decline to 1–2 individuals/ha and failed to recover in the approximately 2.5 years of post-ENSO monitoring. We noticed no signs of sickness or illness among these animals, although adult body masses of D. simulans (but not D. stephensi) declined through the ENSO event, suggesting that food resources for the former species may have been compromised. Alternatively, populations of D. simulans may have been unusually high before the ENSO event, such that the onset of rains merely hastened a predictable winter die-off. Finally, other rodents could have robbed seeds from the food caches of Dulzura kangaroo rats, influencing the ability of the latter to survive the ENSO event. Although this explanation remains speculative, cache pilferage has been demonstrated among other heteromyids, and a recent theoretical study suggests this may be an important mechanism of species coexistence. Further investigations of cache pilferage could enhance our understanding of the ecology and evolution of these diverse small mammal assemblages.