Dendroctonus rhizophagus Thomas & Bright is an endemic bark beetle from northern Mexico. It occurs along the Sierra Madre Occidental and attack young trees of four Pinus species, particularly Pinus engelmanii. In this study, we assess genetic structure and possible association between genetic diversity and geographic distribution. We used spatial analysis of molecular variance (SAMOVA) and nested clade phylogeographic analysis (NCPA) to investigate historical and demographic events that better explains their current distribution. We obtained 70 haplotypes from COI sequences (547 bp long) of adult insects collected from 9 geographic populations. Nucleotide divergence (0.010 ± 0.005) and haplotype diversity (0.975 ± 0.011) suggests that D. rizophagus have experienced a rapid population growth, along with recent accumulation of mutations; as a result of recent expansion events. The Mantel test revealed that there is no correlation between geographical and genetic distances (rMantel=-0.047 P=0.486). This result is supported by SAMOVA analysis, which demonstrated no grouping among populations. The inferences obtained by NCPA analysis for nearby populations suggest an event of restricted gene flow whit isolation by distance. Whereas the total cladogram inference suggests an event of long distance colonization and/or past fragmentation between the population of Campo Nuevo (Chihuahua) and the population of La Manga (Durango). As our data suggest that D. rhizophagus populations does not follows an isolation by distance model, past fragmentation and recent dispersal events better explains their actual genetic differentiation.