Abstract. The Quaternary climate cycles forced species to repeatedly migrate across a continually changing landscape. How these shifts in distribution impacted the evolution of unrelated but ecologically associated taxa has remained elusive due to the stochastic nature of the evolutionary process and variation in species-specific biological characteristics and environmental constraints. To account for the uncertainty in genealogical estimates, we adopted a coalescent approach for testing hypotheses of population divergence in coevolving taxa. We compared genealogies of a specialized herbivorous insect, Parnassius smintheus (Papilionidae), and its host plant, Sedum lanceolatum (Crassulaceae), from the alpine tundra of the Rocky Mountains to null distributions from coalescent simulations to test whether tightly associated taxa shared a common response to the paleoclimatic cycles. Explicit phylogeographic models were generated from geologic and biogeographic data and evaluated over a wide range of divergence times given calibrated mutation rates for both species. Our analyses suggest that the insect and its host plant responded similarly but independently to the climate cycles. By promoting habitat expansion and mixing among alpine populations, glacial periods repeatedly reset the distributions of genetic variation in each species and inhibited continual codivergence among pairs of interacting species. The field of comparative phylogeography attempts to infer the evolutionary history of an ecosystem or an ecological association by comparing genealogical estimates of history from multiple species and thus provides a foundation for understanding the assemblage, structure, and evolution of communities (Bermingham and Moritz 1998;Avise 2000;Arbogast and Kenagy 2001). In most cases, however, analyses have relied on qualitative comparisons, such as describing the history and underlying processes of an ecosystem from common patterns exhibited by several related taxa (e.g., Soltis et al. 1997;Calsbeek et al. 2003). By its very nature, this descriptive approach precludes statistical tests of a priori hypotheses concerning the history of the region in question (Carstens et al. 2005a). In cases where the histories of two distantly related but ecologically associated species (i.e., coevolving hosts and parasites) are of interest, tests have typically taken the form of genealogical comparisons and hunts for evidence of concordance or cospeciation (reviewed in Page and Charleston 1998). However, species-specific biological characteristics have likely prompted independent migrations of species (West 1964(West , 1980Bennett 1990Bennett , 2004Coope 1995;Elias 1996;Whitlock and Bartlein 1997;Taberlet et al. 1998; Hewitt 1999 To evaluate the evolutionary history of distantly related but ecologically associated taxa analyses must accommodate the stochastic variation in genealogies caused by the coalescent process and life-history strategies of each species. So far, only a few comparative studies have taken this approach (e.g., Carsten...