Geographically isolated environments such as the conifer forests atop the Madrean “sky islands” in southeastern Arizona provide natural laboratories for studying factors involved in speciation and origins of biodiversity. Using molecular and geospatial analyses, we examine beetle population phylogeny, regional climate records, and the Quaternary paleobiogeography of forests to evaluate four hypothetical scenarios regarding the current geographic and population genetic patterns of Scaphinotus petersi. Scaphinotus petersi is a large, flightless beetle that resides in the Madrean conifer forests above ~ 1900 m asl. Our results do not support the current hypothesis that S. petersi populations found on seven separate mountain ranges are genetically distinct and separated as temperatures warmed after the Last Glacial Maximum (LGM). Rather, we show that only some of the ranges hold genetically distinct populations, and the timing of separation among the populations does not appear to coincide with specific climatic events such as warming trends. In addition, we show that predicted changes to the climate of the Madrean sky islands may result in the disappearance of S. petersi from some of the lower ranges by the end of this century.