Abstract. In island systems with diverging populations, the history of island formation and genealogical estimates of divergence dates can be mutually informative. In the ''sky islands'' of southeastern Arizona, climate-induced contraction of woodlands appears to have fragmented populations of woodland-dwelling species onto disjunct Climactic oscillations during the Quaternary played a significant role in the formation of genetic diversity and historical demography of numerous plant species in northwestern China. In this study, we used 11 simple sequence repeats derived from expressed sequence tag (EST-SSR), two chloroplast DNA (cpDNA) fragments, and ecological niche modeling (ENM) to investigate the population structure Phylogeography was originally portrayed as the mitochondrial DNA link between these disciplines (Avise et al. 1987). However, phylog eography has since broadened immensely (for a recent review, see Hickerson et al. (2010)), wi th a current focus on gathering multiple gene trees. During the last two decades, since the publication of "Phylogeography: The History and Formation of Species" by John C. Avise (), studies of population genetics at broader time scales gave rise to so-called phylogeography.This discipline establishes that most species in nature exhibit some degree of genetic structure linked to geography (Avise 2000; Richards et al. 2007). Phylogeography infers the demographic history of various species by resolving genetic relationships among populations across a geographic range. Comparison of phylogeographic patterns of multiple species with similar geographic distributions, i.e., comparative phylogeography, allows us to assess the roles of regional historical events and species-specific ecological factors in shaping Using an example based on the boreal mammal fauna of North America we illustrate here: (1) the utility of phylogeography in elucidating contemporary patterns of evolutionary subdivision within species and species complexes and (2) the value of comparative phylogeography in providing novel insights into the relationship between earth history and the phylogeography or migratory footprints of species [7-9,28- 29]. Maternally inherited chloroplast DNA lineages in natural populations often display geographical structure [9], which is useful for deciphering the evolutionary history of species. The cpDNA markers are thought to be the most appropriate Phylogeographic studies focus on understanding the contribution of historical versus contemporary ecological processes in shaping present-day species distributions. Phylogeographic inferences are based on DNA sequences sampled from the same locus in many individuals collected throughout the geographic range of a species. The Quaternary history of species distributed in this region may display divergent characteristics. To this end, we used cpDNA sequences to describe the population structure and investigate the phylogeographic history of R. dauricum in northeastern China. The aims of this study are as follows: (1) examine the genetic diversity A good example of this is the escalating number of DNA-based studies reporting cryptic species [1,2]. Cryptic, or sibling, species are discrete species that are difficult, or sometimes impossible, to distinguish morphologically and thus have been incorre