Sequences of 479 bp region of the mitochondrial COI gene were applied to detect population genetic diversity and structure of Dendroctonus valens populations. By comparing the genetic diversity between native and invasive populations, it was shown that the genetic diversity of Chinese populations was obviously lower than that of native populations with both indices of haplotype diversity and Nei’s genetic diversity, suggesting genetic bottleneck occurred in the invasive process of D. valens, and was then followed by a relatively quick population buildup. According to phylogenetic analyses of haplotypes, we suggested that the origin of the Chinese population was from Califia, USA. Phylogenetic and network analysis of native populations of D. valens revealed strong genetic structure at two distinct spatial and temporal scales in North America. The main cause resulting in current biogeographic patt was supposedly due to recycled glacial events. Meanwhile, a cryptic species might exist in the Mexican and Guatemalan populations.