Background: Climate change is challenging plants and animals not only with increasing temperatures, but also with shortened intervals between extreme weather events. Relatively little is known about diverse assemblages of organisms responding to extreme weather, and even less is known about landscape and life history properties that might mitigate effects of extreme weather. Our aim was to address this knowledge gap using a multi-decadal dataset of 163 butterfly species that recently experienced a millennium-scale drought. To understand faunal dynamics in the context of the millennium drought, we investigated the behavior of phenology (including date of first flight), species richness and diversity indices through time at 10 study sites spanning an elevational gradient. Linear models were developed to understand the differential sensitivity of butterflies to climate at low and high elevations. Results: Dates of first flight advanced across the elevational gradient during the drought, leading to an overall expansion of the flight window at low elevations and a compression of the flight window in the mountains. The number of species observed per year increased at lower elevations but decreased at higher elevations, apparently as a consequence of extreme sensitivity to hot and dry conditions.